I'm running into the same problem after the 2.6 upgrade (from 2.4)
I've enabled the new 'experimental' backup format, so perhaps that will help, as I suspect it might be courses over 4GB that are crashing the backup. In 2.4 it simply failed that course backup, but in 2.6 is it possible it doesn't clean up at all once it hits one of those?
That brings me to the design decisions that may be influencing this: I'd argue it should be creating, copying to target for course backups, and clearing the temp for each course as it completes, if it's not. I've got over 100GB in my Moodle install, and can't float multiple copies of the temp files for the whole mess when backups fail. I understand when dumping files into a tar that a local scratch disk has performance advantages, but either handle the temp files during backup or maybe better let me flip a switch to work on the target as scratch as well?
Don't know if anyone involved in writing watches these threads, or if I should submit that elsewhere for consideration, but thought I'd mention it.
At any rate - I'm curious if you found resolution on this, and what that looked like?