If you add the „Movies“ folder, Plex will not only scan that folder but do so recursively. That means the content of your „Bonus“ folder is scanned because it’s directly added to your library AND because it’s a subfolder of the „Movies“ folder (which is linked to your library as well). Hence you end up with duplicate items.
You should try to avoid adding recursive folders to a library. You can have many folders linked to a library but try to comply with the official naming schema and folder structure inside each top-level library folder.