Normally this should only happen where

a) there is a Program with a recurring course, maybe you should check that all the programs were actually deleted - maybe a different admin created a Program you can't see? The mdl_prog database table should show any still-existing programs.

b) If you are on 2.5 then Certifications are a special type of Program that also have repeating courses. Again they are stored in mdl_prog, the difference between an ordinary Program and a Certification in the database is that Certifications will have an integer in the "certifid" field.