Each copy course would try to create a new course id number.
When you go to your site, and view the category where these copies were to be placed, do you see at the bottom of that category any 'pending' courses?
Make a query of db and of the mdl_task_adhoc table of your DB. If adhoc task are working correctly there should be no records.
mysql> select id,component,nextruntime,faildelay,timecreated,timestarted,firststartingtime from mdl_task_adhoc
If it looks confused, might have to truncate that table ... 'start over'.
And check out what's in moodledata/temp/backup/ failed course copies might be in there - not sure they would give you any clue, but they would be taking up space that you can remove manually.
If you have linux and command line, suggest running the cron.php script from the command line:
cd /path/to/moodlecode/admin/cli/
php cron.php [ENTER]
and see what happens.
'SoS', Ken