Yes. I have seen that occasionally. Rescanning the library fixed it for me. It took a couple of minutes, but Plex put things in the right place.
If that does not work for you, then try Plex Dancing the entire folder - movie and extras. When you clean bundles, go ahead and optimize the database at the same time, since you’re on the same screen (Settings → Troubleshooting).
Also, what version of PMS and what platform?
