Cards you see in your opponent's hand aren't "real" cards - internally, we call the object a RevealedCard. They get created when a known card goes to a hidden zone, and are removed when a card with the same appearance leaves (or the contents of that zone become unknown in some other way, like a Brainstorm effect). RevealedCards should have no impact on actual gameplay, such as effects that count the number of cards in a hand, or selecting a card to discard.
We didn't properly handle making RevealedCards for tokens that have been mutated; they make RevealedCards because the object-on-the-battlefield was a "real card". Clearly, that should be examined on a component-by-component basis. We should fix it this week, I hope, but know that it's only a visual problem. #wotc_staff