I got used to mashing X to run in Red Dead Redemption, and when I switched to Call of Duty I couldn't stop jumping.
Playing God of War, I keep trying to move the camera with the right stick, and end up rolling around like an idiot.
Back when I played Super Smash Brothers Brawl alot, when I played other games I would catch myself trying to "recover" from falling off cliffs.
And now that I play Mortal Kombat alot, I find myself trying to block with R2 in all kinds of different games.