Don't have an answer .... just some things to check.
When you begin that process of copy course, don't click on anything that takes you away from the progress displayed. Stay right there until it completes. If you do, that puts this into a background process and possibly conflicts with other background processes ... some not related to moodle at all!
Background processes can get romped on ... for lack of a better term.
Look at Scheduled task for task that clean up temp or backup areas. Set them to less frequent.
Look in moodledata/temp/backup/
Successful backups of any kind will leave a 0 byte size log file.
Un-successful. backups of any kind will leave a hash named directory with some or all of the backup inside. Change into one of those contenthash named directories and see what's there! (command line or file browser)
IF you see a backup.mbz and a moodle_backup.xml file there it did finish the backup but couldn't (for some reason) do the very last step ... that of copy the backup.mbz. file to destination location.
That backup.mbz file, BTW, is a good backup and could be used to restore.
Sorry ... gotta collect info to even begin to make more suggestions.
'SoS', Ken
by Ken Task.