I've seen this question posted several times so I've done what I can so far.
We have several departments that were imported that should not have been. Mostly because the department name was just wrong or it was a duplicate.
I've gone though each request/asset/requester and made sure any trace of these wrong departments are gone. However when I try to delete the department I still get the message saying "Department is being used by a module. Hence cannot delete it."
I've reached the point where I don't know where else to look for the last few items that give me this message.