Plex Linux has a bug where it picks the first match in the list even if it isn't the correct name. The same python code works on Windows with the same match list so there is something Windows is doing that the Linux version isn't.
/media/movies/Comedy/Office Space (1999).mkv
/media/movies/Drama/Bob's New Suit (2011).mkv
These are marked as duplicates under Linux and through my testing it is because they both come up when doing a match search. Now how these two come up in a search together is anyone's guess, but Windows somehow gets it right and Linux doesn't.
As you can see by the screenshot both movies come up in the search and Linux just auto picks the first match.
Thanks,
Chad