I have seen this several times on both of my v3 servers, in this case the user uploaded over his/her quota, deleted all mp3's and then was not able to upload any new files, the old mp3's were still in the users media library but since you all removed the "update media library" option, and since the user is not able to upload any more mp3's -- there is no way for them to update the library (adding new files automatically updates the library)

http://prntscr.com/m94pl)

SO I cleared all the users files out by running the cron job, he has uploaded no more than 500MEG and his media library is full -- I see he uploaded some invalid files, JPEG and m3u but the size is very small and he is not able to upload any more, again I have also seen this before on a couple accounts, at the time I just deleted and refunded the client but I can't keep doing that
http://prntscr.com/m955u

This is a known issue (pretty sure it was reported here on the forums, in fact) -- the FTP server doesn't trigger a media library update on deletions.  This is not the intended behavior and will be fixed ASAP.

For a temporary workaround, updating the media library from the commandline is all that's needed to fix this.  Or you can manually enter the URL to the old media library update page -- it's no longer linked to nor supported, but it's still there.