Think that only happens when the course you are restoring is already in existence.
Have been cleaning up a 4.1.highest site and was deleting courses (64 to be exact) that had not be used in years when I made a boo-boo and deleted one course that was hidden from view. Prior to deletions I made backups of those hidden courses. Teacher wanted to be able to get resources from that course and asked that it be restored. Restore done via moosh ... it came back in to same category where it was before - hidden - had a new ID - which was expected but no duplication ... course did not exist.
Not sure that moosh uses the same routines/code as the backup/restore scripts found in code/admin/cli/. One way to find out ... install moosh and do just one restore to a category ... that course doesn't exist in that category. You'll find other uses for moosh when it comes to massive stuff.
How old are those courses? (version of Moodle?)
'SoS', Ken