Movie listed many times with multiple parts and different sources

@chyron8472 said:
Third, when you do the Plex Dance, after you move the mishandled files out of your library make sure Plex has removed them before you move them back in again. This is where “Empty Trash Automatically After Every Scan” helps. If you don’t have that enabled, Plex will hold those missing library entries in its database (with trashcan icons) until the Trash is emptied. You want Plex to delete them.

This could be the issue, I’ll try it.