This a quirk in pasting covers. If an mp3 song was added to a folder and doesn't have a cover you can only add a cover from a file. The paste function is grayed out. However, if there is another song with a cover in the folder you can copy the cover and paste it to the new song, delete it, then paste the cover you want into the box. (The paste option appears after a successful paste or insert from a file.)
If a song already has a cover you can paste another over the existing cover and both will exist. Delete one and you'll see the other one is still there.
Ver. 3.28 64 bit