I just moved around a few folders in my library. I then cleaned the library and it kept asking me over and over again if I wanted to remove them or keep them. Might be helpful for a remove all option of some kind. Also, it was cutting off some of the paths.
I'd say it's by design. Not a bug per se
I believe he's referring to XBMC thinking that a missing folder is the same as an offline source, and then asking if you want to clean up the offline source entries, asking once per each library entry (such as once per TV show or movie). I think it's fixed in master.