The issue appeared as soon as we moved the course backup file location (backup_auto_destination) to a separate virtual disk in order to make more space for the moodledatafolder itself. But Moodle started to move the deleted backup files (after the retention time was reached) into the trashdir folder which led to a increase of the moodledata storage.
In December 2011 more ore less the same bug (https://tracker.moodle.org/browse/MDL-30725) was reported and fixed for version 2.0, 2.1 and 2.2. However different users running Moodle 2.5 and 2.6 complained that the bug reappeared in the mentioned versions.
I assume the best solution would be to delete the backups without moving them into the trashdir folder for another 24hours until they get deleted.