Did you have a database error while scanning the collection?
I had one, and I found a few folders that were file names, and empty, so you're not alone.
I deleted the database file and just ran it again without any hiccups so maybe that fixed it. The database file is rhythmdb.xml and it's in ~/.local/share/rhythmbox/
maybe that will help. I don't see any new folders after doing it.
Home folder then Ctrl+h then go to .local > share > rhythmbox