First, do you really have duplicates, or is it the music app being dumb? Look at the information for a couple of duplicate tracks and see whether they are in different places. If they are then removing one copy, or telling the music app not to include one of those locations in its search path, should fix that.
However, be wary. In case you don't know, Android can have different paths pointing to the same file. For example, /sdcard/Music and /storage/emulated/0/Music are the same folder, so deleting a file from one of these deletes "both copies" (because there is actually only one copy). Some music apps may, if configured wrong, treat different paths to the same file as different copies, resulting in "duplication". This is what I meant by the app being dumb. So if this is the case you need to tell it not to look in one of those places for the music rather than deleting copies.