by Ken Task.
Cron job and scheduled task?
/admin/tool/task/scheduledtasks.php
There are several for 'cleanup' + automated backups.
Your issue might be in overlap of a clean up and automated backups that happened to be running at the time.
Any references in web server error logs about locks? Locks supposedly prevent some action from taking place
while a task/process is running ... like auto backup of courses and clean up of Automated backups area ... moodledata/temp/backup/... there should only be .log files
If all were successful.
If failure happens with same course, inspect the course itself and see if you can make a backup from the course admin menu.
No set/pat answer ... must explore! :|
'SoS', Ken