diff --git a/crates/aof-core/src/registry.rs b/crates/aof-core/src/registry.rs
index ea6ecc2..60231cb 100644
--- a/crates/aof-core/src/registry.rs
+++ b/crates/aof-core/src/registry.rs
@@ -72,6 +72,12 @@ impl Registry<AgentConfig> for AgentRegistry {
             let file_path = entry.path();
 
             if file_path.extension().map_or(false, |e| e == "yaml" || e == "yml") {
+                // Skip non-Agent YAML files (Trigger, Fleet, Flow, etc.)
+                if !yaml_file_has_kind(&file_path, "Agent") {
+                    tracing::debug!("Skipping non-Agent file: {:?}", file_path);
+                    continue;
+                }
+
                 match load_yaml_file::<AgentConfig>(&file_path) {
                     Ok(agent) => {
                         let name = agent.name.clone();
@@ -663,6 +669,26 @@ fn load_yaml_file<T: serde::de::DeserializeOwned>(path: &Path) -> AofResult<T> {
     Ok(resource)
 }
 
+/// Check if a YAML file has a specific `kind` field value
+/// Returns true if the file has the expected kind, false otherwise
+fn yaml_file_has_kind(path: &Path, expected_kind: &str) -> bool {
+    // Helper struct to just parse kind field
+    #[derive(serde::Deserialize)]
+    struct KindCheck {
+        kind: Option<String>,
+    }
+
+    let content = match std::fs::read_to_string(path) {
+        Ok(c) => c,
+        Err(_) => return false,
+    };
+
+    match serde_yaml::from_str::<KindCheck>(&content) {
+        Ok(check) => check.kind.as_deref() == Some(expected_kind),
+        Err(_) => false,
+    }
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
diff --git a/crates/aof-triggers/src/handler/mod.rs b/crates/aof-triggers/src/handler/mod.rs
index 3f4b510..123a194 100644
--- a/crates/aof-triggers/src/handler/mod.rs
+++ b/crates/aof-triggers/src/handler/mod.rs
@@ -767,6 +767,12 @@ impl TriggerHandler {
                 continue;
             }
 
+            // Check if file has kind: Agent before trying to parse
+            if !Self::yaml_file_has_kind(&path, "Agent") {
+                debug!("Skipping non-Agent file: {:?}", path);
+                continue;
+            }
+
             // Try to load as agent
             match runtime.load_agent_from_file(path.to_str().unwrap()).await {
                 Ok(agent_name) => {
@@ -774,8 +780,8 @@ impl TriggerHandler {
                     count += 1;
                 }
                 Err(e) => {
-                    // Not all YAML files are agents, this is fine
-                    debug!("Skipping {:?}: {}", path, e);
+                    // Agent file failed to parse - this is a real error
+                    warn!("Failed to load agent from {:?}: {}", path, e);
                 }
             }
         }
@@ -787,6 +793,24 @@ impl TriggerHandler {
         Ok(count)
     }
 
+    /// Check if a YAML file has a specific `kind` field value
+    fn yaml_file_has_kind(path: &std::path::Path, expected_kind: &str) -> bool {
+        #[derive(serde::Deserialize)]
+        struct KindCheck {
+            kind: Option<String>,
+        }
+
+        let content = match std::fs::read_to_string(path) {
+            Ok(c) => c,
+            Err(_) => return false,
+        };
+
+        match serde_yaml::from_str::<KindCheck>(&content) {
+            Ok(check) => check.kind.as_deref() == Some(expected_kind),
+            Err(_) => false,
+        }
+    }
+
     /// Register a platform
     pub fn register_platform(&mut self, platform: Arc<dyn TriggerPlatform>) {
         let name = platform.platform_name();
diff --git a/crates/aofctl/src/commands/run.rs b/crates/aofctl/src/commands/run.rs
index 097c315..5498aec 100644
--- a/crates/aofctl/src/commands/run.rs
+++ b/crates/aofctl/src/commands/run.rs
@@ -27,7 +27,33 @@ struct K8sMetadata {
 
 /// Parse agent config with detailed error messages including field path and line numbers
 fn parse_agent_config(content: &str, file_path: &str) -> Result<AgentConfig> {
-    // First, try the normal parse
+    // First, check if this is the right kind of resource
+    #[derive(serde::Deserialize)]
+    struct KindCheck {
+        kind: Option<String>,
+    }
+
+    if let Ok(check) = serde_yaml::from_str::<KindCheck>(content) {
+        if let Some(kind) = check.kind {
+            if kind != "Agent" {
+                let hint = match kind.as_str() {
+                    "Trigger" => "Triggers are used with 'aofctl serve', not 'aofctl run'".to_string(),
+                    "Fleet" => "Use 'aofctl run fleet <file>' to run a fleet".to_string(),
+                    "Flow" | "AgentFlow" => "Use 'aofctl run flow <file>' to run a flow".to_string(),
+                    "Workflow" => "Use 'aofctl run workflow <file>' to run a workflow".to_string(),
+                    _ => format!("This file contains a {} resource, not an Agent", kind),
+                };
+                return Err(anyhow!(
+                    "Wrong resource type: {}\n\n  Expected: kind: Agent\n  Found: kind: {}\n\n  Hint: {}\n",
+                    file_path,
+                    kind,
+                    hint
+                ));
+            }
+        }
+    }
+
+    // Now try the normal parse
     let deserializer = serde_yaml::Deserializer::from_str(content);
     let result: Result<AgentConfig, _> = serde_path_to_error::deserialize(deserializer);