Bummer, and tedious to fix.
Go to the Assignments page to identify the duplicates and delete or unpublish them from there. What I do is.............
Problem is, that you might have had students submitting to both copies of an assignment. Canvas will not let you unpublish any assignment with a submission. This is where it can get tedious, because you will need to manually move scores into the version you want to keep. Identifying duplicates is really best done before students start using the course.
I hope this helps,