Sorry, cannot do a Vulcan Mind Meld (StarTrek/Spock) with a remote system.
Obviously, Moodle is trying to keep track of what failed and attempts again ... but, let's deal with preventing it from crashing right now knowing that we're trading off individual course backups (which I know is desired) to one of site backups.
First, turn automated backups to manual.
Install an add on called courses sizes. It's not accurate, but good enough for our purposes. We just need to see the largest courses and work with backing up those with the CLI script.
In the automated backups one has no control over which courses to exclude and when ... so let's say it's course ID 5 that's failing ... and causes issues with the remaining 50 - 6-50.
That's the course then (ID 5) to use with the CLI backup script.
Automated backups as well as the CLI backup script do take parameters you've set in the backups settings for the site.
http://yoursite/admin/settings.php?section=backupgeneralsettings
Consider reducing the number of days for logs ... or no logs at all in backups.
Consider other items such as: including users or not ... excluding them would also mean there are no assignments submitted by them in the backup. That has to reduce the backup size ... thus time to create the backup, space needed to create the backup and archive etc.
Get a base course backup for troublesome course, then change those settings back to what is desire. At least, now, you have some backup of the course ... even though it has no users no logs, no grades, etc.. - kinda like a re-set course. That backup could be your fall back position (last resort).
'spirit of sharing', Ken