Check your project files for symlink references to local files, which in some cases seems to cause CodeKit to loop on adding those files.
One example from a recent project of mine:
index.php -> run-all-tests.php
run-all-tests.php
This resulted in CodeKit adding run-all-tests.php
thousands of times. I suspect that it may only result if the natural file ordering places the symlink before the real file, or if it is in the same folder (as I don't see it happen in all cases).
To fix: remove the symlink, or you can exclude the file/folders from compilation.