It’s about photos in the Photos app that were not properly deleted, not photo files. The Photos app has an internal analog to the trashcan. When you delete a photo, the photo is removed from the normal photos index and moved to a Recently Deleted list. After 30 days, the actual photo file will be deleted if you don’t change your mind. There is an automated process that looks for photos tagged for deletion and deletes them on schedule.

There has been an unknown bug for a few years where, sometimes, the process that is supposed to tag the photo for deletion removes it from the list but doesn’t add the right tag for deletion and the schedule process never noticed them and never told the OS to delete the files. They just sat there in the photos library folder, sometimes for years.

The files were never actually deleted, just removed from the photos list. Later another process was deployed that saw unreferenced photos and added them into the photos index. That freaked some people out, particularly if they really had wanted to get rid of those photos.

This all happened as a higher level than the OS. The OS file deletion process was never invoked for these photos.