I'd double check what the paths are in your library. If you're inadvertently telling plex to search /mnt for the library then it will pick up everything
If you're actually telling it to only look in /mnt/user/.... then if it's scanning the parent (/mnt) for media then it's a Plex bug and needs to be reported in their own forums (IMO this is unlikely)
IMO, the most secure system is to map only the shares you need Plex to have access to (eg: /movies1 to /mnt/user/movies1, /movies2 to /mnt/user/movies2 etc). What you're effectively doing is letting Plex have access to all of your banking information (which are stored in /mnt/user/Banking), those "private" pictures of your wife stored in xXx etc. Up to you, but if Plex doesn't require access to the stuff you actually don't want it to have access to, don't give it access