Currently when using the Manage assignments option for an Intune app/update in the Publisher, you are able to both add and remove assignments. However, when you run the sync it will add any new assignments to the Intune app but not remove any. This means you are left with unwanted assignments.
The expected behaviour is that the assignments are actually removed from the Intune app, as they are when you do the same thing using the Intune App Manager.