I remember how everytime I played Ratchet and Clank then Jak and Daxter, I would get both of their controls mixed up and it would frustrate me everytime.
I got Killzone 3 and uncharted 2 mixed up when i used to play them
I don't know why but if I'm off Uncharted 3 for like more than 3 days or so, I have to get back into it.
For some reason I like doing the "tap-a-nade" trick or what have you Big2Krew showed before a lot more than just aiming it with my gun. It works wonders most of the time, but bank'n'boom is still useful.
But I know how you feel, I played RE6, went back to Uncharted 3 and was like, "Lolwat, this isn't Resident Evil."
Unless your a new player you should remember how to do every action without much thought.
Muscle memory, as mentioned earlier. You know what the buttons are, and you assume that you do know it by instinct because you know them. Problem is, your hands went all GTA4 mode/Max Payne 3 mode/some-other-game mode and instinctively presses buttons your mind was processing (like crouching or taking cover) on the wrong layout (circle, you SOB.)
It's nothing more than muscle memory. It's like telling someone where things are on a keyboard without the keys being labeled. You wouldn't be able to remember as easily by looking at it as you would by putting your hands on the keys. It's essentially saying that you've played the game enough that pressing a button is a conditioned response rather than a thought requiring process. For me personally it happens with all games and within a few plays of the game. After that I can go to another game and come back and it will naturally come back to me. Just don't ask me how to reload cause I'll be silent for a few seconds while I force myself to not say Square from playing other games.