by Gilles-Philippe Leblanc.
We have a similar problem but we found that the backups from deleted courses was not purged.
I just created a plugin to remove this kind of backups:
https://github.com/leblangi/moodle-tool_purgeautobackups
Also, you may vote on this task:
https://tracker.moodle.org/browse/MDL-48808
I hope this will help.