That is interesting because Hero AT's and Villain AT's are Badge Specific, meaning that you should'nt be seeing any Badges that are Villain Only, under your Heroes' Manage Badges Pages.
We are aware of some of the Badges missing, but only for some of the VEAT types. We've not encountered this for any other AT types, until you came forth. Can you give us specifics, such as:
What Toon(s) are you seeing this with? (Name and Alignment)
What Badges are showing up that should not be?
What Badges are just not showing up?
That will help us get closer to the cause of this.