diff --git a/PythonScripts/audit_translations/auditor.py b/PythonScripts/audit_translations/auditor.py
index dd0c68ae..0fac4d2a 100644
--- a/PythonScripts/audit_translations/auditor.py
+++ b/PythonScripts/audit_translations/auditor.py
@@ -191,19 +191,67 @@ def issue_base(rule: RuleInfo, file_name: str, language: str) -> dict:
 def first_structure_mismatch(
     english_tokens: List[str],
     translated_tokens: List[str],
-) -> Tuple[Optional[str], Optional[str]]:
+) -> Tuple[Optional[str], Optional[str], int]:
+    """
+    Find the first structural mismatch between two token lists.
+
+    Returns (en_token, tr_token, mismatch_position).
+    Position is the index in the token list where they first differ.
+    """
     min_len = min(len(english_tokens), len(translated_tokens))
     for idx in range(min_len):
         if english_tokens[idx] != translated_tokens[idx]:
-            return english_tokens[idx], translated_tokens[idx]
+            return english_tokens[idx], translated_tokens[idx], idx
     if len(english_tokens) > min_len:
-        return english_tokens[min_len], None
+        return english_tokens[min_len], None, min_len
     if len(translated_tokens) > min_len:
-        return None, translated_tokens[min_len]
-    return None, None
+        return None, translated_tokens[min_len], min_len
+    return None, None, -1
+
+
+def resolve_issue_line_at_position(
+    rule: RuleInfo,
+    kind: str,
+    token: Optional[str] = None,
+    position: int = 0
+) -> Optional[int]:
+    """
+    Resolve the line number for a specific occurrence of an element within a rule.
+
+    Args:
+        rule: The rule to search in
+        kind: The kind of element ('match', 'condition', 'variables', 'structure')
+        token: For structure kind, the specific token to find
+        position: The occurrence index (0 for first, 1 for second, etc.)
+
+    Returns:
+        The line number if found, None if the element doesn't exist at that position.
+    """
+    if kind == "match":
+        lines = rule.line_map.get("match", [])
+    elif kind == "condition":
+        lines = rule.line_map.get("condition", [])
+    elif kind == "variables":
+        lines = rule.line_map.get("variables", [])
+    elif kind == "structure" and token:
+        token_key = f"structure:{token.rstrip(':')}"
+        lines = rule.line_map.get(token_key, [])
+    else:
+        lines = []
 
+    if position < len(lines):
+        return lines[position]
+    return None
 
-def resolve_issue_line(rule: RuleInfo, kind: str, token: Optional[str] = None) -> int:
+
+def resolve_issue_line(rule: RuleInfo, kind: str, token: Optional[str] = None) -> Optional[int]:
+    """
+    Resolve the line number for an issue within a rule.
+
+    Returns the line number if found, None if the element doesn't exist in the rule.
+    For 'structure' kind with a missing token, returns None instead of falling back
+    to rule.line_number to avoid misleading line numbers when elements are missing.
+    """
     if kind == "match":
         lines = rule.line_map.get("match", [])
     elif kind == "condition":
@@ -213,6 +261,9 @@ def resolve_issue_line(rule: RuleInfo, kind: str, token: Optional[str] = None) -
     elif kind == "structure" and token:
         token_key = f"structure:{token.rstrip(':')}"
         lines = rule.line_map.get(token_key, [])
+        # For structure differences, if the token doesn't exist, return None
+        # rather than falling back to rule.line_number which is misleading
+        return lines[0] if lines else None
     else:
         lines = []
     return lines[0] if lines else rule.line_number
@@ -274,9 +325,21 @@ def collect_issues(
         if diff.diff_type == "structure":
             en_tokens = extract_structure_elements(diff.english_rule.data)
             tr_tokens = extract_structure_elements(diff.translated_rule.data)
-            en_token, tr_token = first_structure_mismatch(en_tokens, tr_tokens)
+            en_token, tr_token, mismatch_pos = first_structure_mismatch(en_tokens, tr_tokens)
+
+            # Skip reporting when tokens are misaligned (both exist but differ)
+            # This avoids misleading line numbers when entire blocks are missing/added
+            # We only report when one is None (clear case of missing element)
+            if en_token is not None and tr_token is not None and en_token != tr_token:
+                continue
+
             issue_line_en = resolve_issue_line(diff.english_rule, "structure", en_token)
             issue_line_tr = resolve_issue_line(diff.translated_rule, "structure", tr_token)
+
+            # Skip reporting structure differences where we can't find both tokens
+            # This avoids misleading line numbers when blocks are missing
+            if issue_line_en is None or issue_line_tr is None:
+                continue
         else:
             issue_line_en = resolve_issue_line(diff.english_rule, diff.diff_type)
             issue_line_tr = resolve_issue_line(diff.translated_rule, diff.diff_type)
@@ -340,23 +403,37 @@ def print_warnings(result: ComparisonResult, file_name: str, verbose: bool = Fal
                 issues += 1
 
     if result.rule_differences:
-        total_diffs = len(result.rule_differences)
-        console.print(
-            f"\n  [magenta]≠[/] [bold]Rule Differences[/] "
-            f"[[magenta]{total_diffs}[/]] [dim](structural differences between en and translation)[/]"
-        )
+        # Count only diffs that will actually be displayed
+        displayable_diffs = []
         for diff in result.rule_differences:
             if diff.diff_type == "structure":
                 en_tokens = extract_structure_elements(diff.english_rule.data)
                 tr_tokens = extract_structure_elements(diff.translated_rule.data)
-                en_token, tr_token = first_structure_mismatch(en_tokens, tr_tokens)
+                en_token, tr_token, mismatch_pos = first_structure_mismatch(en_tokens, tr_tokens)
+
+                # Skip reporting when tokens are misaligned (both exist but differ)
+                # This avoids misleading line numbers when entire blocks are missing/added
+                if en_token is not None and tr_token is not None and en_token != tr_token:
+                    continue
+
                 line_en = resolve_issue_line(diff.english_rule, "structure", en_token)
                 line_tr = resolve_issue_line(diff.translated_rule, "structure", tr_token)
+                # Skip structure diffs where we can't find both tokens
+                if line_en is None or line_tr is None:
+                    continue
             else:
                 line_en = resolve_issue_line(diff.english_rule, diff.diff_type)
                 line_tr = resolve_issue_line(diff.translated_rule, diff.diff_type)
-            print_diff_item(diff, line_en=line_en, line_tr=line_tr, verbose=verbose)
-            issues += 1
+            displayable_diffs.append((diff, line_en, line_tr))
+
+        if displayable_diffs:
+            console.print(
+                f"\n  [magenta]≠[/] [bold]Rule Differences[/] "
+                f"[[magenta]{len(displayable_diffs)}[/]] [dim](structural differences between en and translation)[/]"
+            )
+            for diff, line_en, line_tr in displayable_diffs:
+                print_diff_item(diff, line_en=line_en, line_tr=line_tr, verbose=verbose)
+                issues += 1
 
     if result.extra_rules:
         console.print(f"\n  [blue]ℹ[/] [bold]Extra Rules[/] [[blue]{len(result.extra_rules)}[/]] [dim](may be intentional)[/]")
diff --git a/PythonScripts/audit_translations/tests/fixtures/de/structure_misaligned.yaml b/PythonScripts/audit_translations/tests/fixtures/de/structure_misaligned.yaml
new file mode 100644
index 00000000..36e3097d
--- /dev/null
+++ b/PythonScripts/audit_translations/tests/fixtures/de/structure_misaligned.yaml
@@ -0,0 +1,15 @@
+- name: misaligned-structure
+  tag: root
+  match: "."
+  replace:
+  - test:
+      if: $Setting = 'Value'
+      then:
+      - test:
+          if: parent::m:minus
+          then: [T: "negativ"]
+          else: [T: "positiv"]
+  - test:
+      if: "*[2][.='2']"
+      then: [T: "quadrat"]
+      else: [T: "andere"]
diff --git a/PythonScripts/audit_translations/tests/fixtures/de/structure_missing_else.yaml b/PythonScripts/audit_translations/tests/fixtures/de/structure_missing_else.yaml
new file mode 100644
index 00000000..445f0670
--- /dev/null
+++ b/PythonScripts/audit_translations/tests/fixtures/de/structure_missing_else.yaml
@@ -0,0 +1,7 @@
+- name: missing-else-block
+  tag: root
+  match: "."
+  replace:
+  - test:
+      if: "@intent='foo'"
+      then: [T: "hat foo"]
diff --git a/PythonScripts/audit_translations/tests/fixtures/en/structure_misaligned.yaml b/PythonScripts/audit_translations/tests/fixtures/en/structure_misaligned.yaml
new file mode 100644
index 00000000..e4999d95
--- /dev/null
+++ b/PythonScripts/audit_translations/tests/fixtures/en/structure_misaligned.yaml
@@ -0,0 +1,18 @@
+- name: misaligned-structure
+  tag: root
+  match: "."
+  replace:
+  - test:
+      if: "$Verbosity!='Terse'"
+      then: [t: "the"]
+  - test:
+      if: "$Setting = 'Value'"
+      then:
+      - test:
+          if: "parent::m:minus"
+          then: [t: "negative"]
+          else: [t: "positive"]
+  - test:
+      if: "*[2][.='2']"
+      then: [t: "square"]
+      else: [t: "other"]
diff --git a/PythonScripts/audit_translations/tests/fixtures/en/structure_missing_else.yaml b/PythonScripts/audit_translations/tests/fixtures/en/structure_missing_else.yaml
new file mode 100644
index 00000000..a1016856
--- /dev/null
+++ b/PythonScripts/audit_translations/tests/fixtures/en/structure_missing_else.yaml
@@ -0,0 +1,8 @@
+- name: missing-else-block
+  tag: root
+  match: "."
+  replace:
+  - test:
+      if: "@intent='foo'"
+      then: [t: "has foo"]
+      else: [t: "no foo"]
diff --git a/PythonScripts/audit_translations/tests/golden/jsonl/de.json b/PythonScripts/audit_translations/tests/golden/jsonl/de.json
index f5c4600f..66cb0214 100644
--- a/PythonScripts/audit_translations/tests/golden/jsonl/de.json
+++ b/PythonScripts/audit_translations/tests/golden/jsonl/de.json
@@ -145,6 +145,42 @@
     "untranslated_texts": [],
     "_explanation": "rule_difference structure_empty.yaml struct-empty|mi"
   },
+  {
+    "language": "de",
+    "file": "structure_misaligned.yaml",
+    "rule_name": "misaligned-structure",
+    "rule_tag": "root",
+    "rule_key": "misaligned-structure|root",
+    "issue_line_en": 6,
+    "issue_line_tr": 6,
+    "rule_line_en": 1,
+    "rule_line_tr": 1,
+    "issue_type": "rule_difference",
+    "diff_type": "condition",
+    "description": "Conditions differ",
+    "english_snippet": "$Setting = 'Value', $Verbosity!='Terse', *[2][.='2'], parent::m:minus",
+    "translated_snippet": "$Setting = 'Value', *[2][.='2'], parent::m:minus",
+    "untranslated_texts": [],
+    "_explanation": "structure_misaligned.yaml: English has extra test block causing misalignment. Fix filters out misleading structure differences but reports condition difference."
+  },
+  {
+    "language": "de",
+    "file": "structure_missing_else.yaml",
+    "rule_name": "missing-else-block",
+    "rule_tag": "root",
+    "rule_key": "missing-else-block|root",
+    "issue_line_en": 8,
+    "issue_line_tr": 1,
+    "rule_line_en": 1,
+    "rule_line_tr": 1,
+    "issue_type": "rule_difference",
+    "diff_type": "structure",
+    "description": "Rule structure differs (test/if/then/else blocks)",
+    "english_snippet": "replace: test: if: then: else:",
+    "translated_snippet": "replace: test: if: then:",
+    "untranslated_texts": [],
+    "_explanation": "structure_missing_else.yaml: Verifies fix still reports legitimate missing else blocks. Unlike misaligned case, this has clear missing element."
+  },
   {
     "language": "de",
     "file": "unicode.yaml",
diff --git a/PythonScripts/audit_translations/tests/test_auditor.py b/PythonScripts/audit_translations/tests/test_auditor.py
index 6b452014..6fcc5e07 100644
--- a/PythonScripts/audit_translations/tests/test_auditor.py
+++ b/PythonScripts/audit_translations/tests/test_auditor.py
@@ -219,3 +219,136 @@ def test_print_warnings_includes_snippets_when_verbose() -> None:
     output = capture.get()
 
     assert output == golden_path.read_text(encoding="utf-8")
+
+
+def test_misaligned_structure_differences_are_skipped() -> None:
+    """
+    Test that structure differences with misaligned tokens are skipped.
+
+    When English has a "test" block that Norwegian doesn't have (and vice versa),
+    the structural tokens become misaligned. The fix skips reporting these
+    to avoid showing confusing line numbers.
+    """
+    base_dir = Path(__file__).parent
+    fixtures_dir = base_dir / "fixtures"
+
+    result = compare_files(
+        str(fixtures_dir / "en" / "structure_misaligned.yaml"),
+        str(fixtures_dir / "de" / "structure_misaligned.yaml"),
+    )
+
+    # The result should detect that structures differ
+    assert len(result.rule_differences) > 0
+    assert any(diff.diff_type == "structure" for diff in result.rule_differences)
+
+    # But when collecting issues, misaligned structure diffs should be filtered out
+    issues = collect_issues(result, "structure_misaligned.yaml", "de")
+    structure_issues = [i for i in issues if i["diff_type"] == "structure"]
+
+    # CRITICAL: Before the fix, this would have structure issues with misleading line numbers
+    # After the fix, misaligned structures are skipped, so we should have 0 structure issues
+    assert len(structure_issues) == 0, (
+        "Expected misaligned structure differences to be filtered out, "
+        f"but found {len(structure_issues)} structure issues"
+    )
+
+    # Other differences (like conditions) should still be reported
+    condition_issues = [i for i in issues if i["diff_type"] == "condition"]
+    assert len(condition_issues) > 0, "Expected condition differences to still be reported"
+
+
+def test_missing_else_block_is_still_reported() -> None:
+    """
+    Test that legitimate missing structural elements are still reported.
+
+    When one file has an 'else' block and the other doesn't, this is a clear
+    structural difference that should be reported with accurate line numbers.
+    """
+    base_dir = Path(__file__).parent
+    fixtures_dir = base_dir / "fixtures"
+
+    result = compare_files(
+        str(fixtures_dir / "en" / "structure_missing_else.yaml"),
+        str(fixtures_dir / "de" / "structure_missing_else.yaml"),
+    )
+
+    # Should detect structure difference
+    assert len(result.rule_differences) > 0
+    structure_diffs = [diff for diff in result.rule_differences if diff.diff_type == "structure"]
+    assert len(structure_diffs) == 1
+
+    # This case has one token None (missing else), so it should still be reported
+    issues = collect_issues(result, "structure_missing_else.yaml", "de")
+    structure_issues = [i for i in issues if i["diff_type"] == "structure"]
+
+    # CRITICAL: This legitimate difference should still be reported
+    # One file has else:, the other doesn't - a clear missing element
+    assert len(structure_issues) == 1, (
+        "Expected missing else block to be reported, "
+        f"but found {len(structure_issues)} structure issues"
+    )
+
+    # Verify the issue has proper line numbers
+    issue = structure_issues[0]
+    assert issue["issue_line_en"] is not None
+    # When else: doesn't exist in translation, we fall back to the rule line number
+    assert issue["issue_line_tr"] == 1  # start of the rule
+
+
+def test_print_warnings_skips_misaligned_structures() -> None:
+    """
+    Test that print_warnings doesn't display misaligned structure differences.
+    """
+    base_dir = Path(__file__).parent
+    fixtures_dir = base_dir / "fixtures"
+
+    result = compare_files(
+        str(fixtures_dir / "en" / "structure_misaligned.yaml"),
+        str(fixtures_dir / "de" / "structure_misaligned.yaml"),
+    )
+
+    # Raw result should have structure differences detected
+    structure_diffs = [diff for diff in result.rule_differences if diff.diff_type == "structure"]
+    assert len(structure_diffs) > 0
+
+    with console.capture() as capture:
+        issues_count = print_warnings(result, "structure_misaligned.yaml", verbose=False)
+    output = capture.get()
+
+    # CRITICAL: The output should not contain "Rule structure differs"
+    # because misaligned structures are filtered during display
+    assert "Rule structure differs" not in output, (
+        "Expected misaligned structure differences to be filtered from display"
+    )
+
+    # The issues count should not include filtered structure differences
+    # It should only count the condition differences
+    condition_diffs = [diff for diff in result.rule_differences if diff.diff_type == "condition"]
+    assert issues_count == len(condition_diffs), (
+        f"Expected issues_count ({issues_count}) to equal condition_diffs ({len(condition_diffs)})"
+    )
+
+
+def test_print_warnings_still_shows_missing_else() -> None:
+    """
+    Test that print_warnings still displays legitimate missing elements.
+    """
+    base_dir = Path(__file__).parent
+    fixtures_dir = base_dir / "fixtures"
+
+    result = compare_files(
+        str(fixtures_dir / "en" / "structure_missing_else.yaml"),
+        str(fixtures_dir / "de" / "structure_missing_else.yaml"),
+    )
+
+    with console.capture() as capture:
+        issues_count = print_warnings(result, "structure_missing_else.yaml", verbose=False)
+    output = capture.get()
+
+    # CRITICAL: This legitimate difference should appear in output
+    assert "Rule structure differs" in output, (
+        "Expected missing else block to be shown in output"
+    )
+
+    # Should report exactly 1 issue (the structure difference)
+    assert issues_count == 1, f"Expected 1 issue but got {issues_count}"