as i said, you have the same file added using 2 different paths. MB doesnt decide by itself to randomly add the same file using 2 different paths.
The new "exclude" button only applies to monitoring of new files.
I suggest you sort the main panel by folder path, remove the links you dont want and then make sure all the places you add files to the library from eg. manual folder monitor, continous monitor, drag/drop from windows explorer etc are added from the same path
edit:
i will enhance the new "Exclude" to prompt to remove existing files from the library