I have an example from before the new version of the Photos app came out. This might have changed since then.
If I take a bunch of photos and then send some of them through Hangouts before I get home to my WiFi those photos doesn't get backed up. I'm guessing it's because Hangouts uses G+ albums for the photos, so technically the photos are on Google's servers, but they're not where I expect them to be (in Auto backup).
scenario:
uploading a bunch of video files all named in the same pattern
when coming back to the google photo interface to put those files in the same group, searching their name does not return the full list, only part of it.
Only by searching "recently added" I can then find and add the missing files.
If you have concrete examples I could investigate.