New update upload did not update all files?

I have finished an update for one of my scripts on CodeCanyon, updated it by submitting the archive with the script. The update has been approved and SOME of the files from the archive I submitted were changed, but some were not.

Has this happened to anyone else (uploading an archive but only some files from that archive being updated)?

This made some customers angry as they installed the new versions but it was not working as expected.