There is an issue on the Windows board that is the same as this (screen shots included in that post). Posting here because I'm having the same issue on my Mac Plex Media Server.
I've experienced it with Close Encounters Ultimate Edition. There are 3 versions, Theatrical, Special Edition, and Director's cut. If I include all 3 versions in the movie folder, Plex recognizes 3 versions but no local extras (local extras are stored in subfolders). If I take 2 versions out of the movie folder, the local extras show up.____