People successfully sued Nintendo for injuries sustained while rotating the control stick during various Mario Party minigames. Nintendo actually lost and had to pay out some money to over-zealous gamers.
There was a multiplayer mode planned in Banjo-Tooie thatd let the second player use Devil Bottles to take control of enemies and even bosses to attack the first player. It didn't make the cut though. It's still in the game's code, however.
In Pokemon Stadium, the designers messed up Electabuzz, giving him an extra finger on each hand.