If the position of the defender is indeed a penalty, let it happen, call it... and allow the other team the opportunity to accept or decline the penalty.
If this is a "prior to the snap" penalty like 12 men in the huddle or a false start, the penalty should be automatic. I guess you could argue that the guy would have backed out of position before the snap. But if he is not supposed to be there in the first place, then it should be called.