So what does one see in /moodledata/temp/backup folder?
Know (from experience) removing files manually contained in /temp/backup/ have no ill affect on Moodle.
Just a guess cause not experienced the same issue ... but ...
Read somewhere in forums/docs that the filesdir is cleaned up by moving unlinked files to the trashdir and then removed (that's done by cron job) ... every four days, by default (?). The automated backups run at a time where the references have been removed but trashdir has not be dumped (?). Automated backups is also run via cron.
Test sites, even if setup exactly as server, don't get used by users - thus things like filesdir would be different. See in one of the lines reported 'draft'. Wonder if that has something to do with it.
'spirit of sharing', Ken