It sounds like you're referring to Barty Crouch Jr villain card.
Unfortunately, the rulebook doesn't go into the specific use-case when defeating other villains. Luckily, the designers have added some FAQ clarifications. In the Boardgamegeek thread: Barty vs Dementor, a similar question is asked and answered by the designer:
... if one has an ability preventing the Heroes from doing something, they do not gain the reward from defeating another Villain.
- Andrew Wolf (Designer)
If Barty Crouch Jr is in play and your team was to defeat a villain whose reward would allow you to remove a token from a location, Barty Crouch Jrs ability may not allow you to.
Villain effects will affect villain rewards.