If two different files have exactly the same content, they will both get cached to the same cache file.
This can happen most frequently when multiple packages require different versions of a given node_module. That is, foo requires bar@1.2.3, and baz requires bar@2.3.4, so the content of the file at "node_modules/foo/node_modules/bar/lib/thing.js" is the exact same as the content of the file at "node_modules/baz/node_modules/bar/lib/thing.js" even though they are different files.