I had this issue a few years ago with a site I inherited. It had over 25,000 such files on a relatively small site sucking up several Gigs of space. I ended up writing some SQL to show me such files, then assigned them to the users to manually clean from their courses. They of course did not realize that appearing to delete a file did not actually delete the file since that would too sensible 
I think an admin level tool to manage for this would be very valuable.
I think an admin level tool to manage for this would be very valuable.