The menu duplication is common problem with WordPress if you imported multiple times. The way to overcome the same is to delete all menus after you are done with your import and then do one last import to restore the menus to original settings.
You can delete menus in Appearance > Menus – select the menu that you want to delete and then click “Delete Menu”. You will be able to delete each set like this .
After deleting whole menus pls do one last import to restore the menus to original settings.