Compare the file locations of one of the duplicates (highlight the file, edit the file [SHIFT+ENTER], Properties, Location). Are they different to their corresponding files? If so, are the duplicates showing up as dead links? If they are showing up as dead links, that means your path has changed and you can sort your collection by Path (right click header row > Set Displayed Fields > add Path > Click the Path column) and remove the dead links from there. Using Manage Duplicates (Musicbee > Tools > Manage Duplicates), you can hide the duplicates, I don't think that's an ideal solution.