I read the instructions as saying that turn order is stepwise. Once you've resolved the villain card, it does not affect you again during that turn, unless the effect is clearly stated as continuous (i.e., heroes cannot draw a card until villain is defeated).
That's how I play it too. Riddle activates his ability at the beginning of the turn and that's it.
For some reason, our biggest problem is remembering
the first two steps of turn order (dark arts card, villain card) and not just going into hero actions. It reminds me a little of the crossroads cards in Dead of Winter. We forget those, too.
We do that all the time too. You spend your down time planning exactly what you're going to do, in what order, and it's going to be super great. So your turn rolls around and you just want to jump right into it, and you forget the dark arts completely.