My dad lent me his car but I did something stupid with; I scratched the car (not very much). After I came back home and because I did something bad to his car I was acting very kindly with him. He looked at me with this smile and he knew that this smile meant something bad so he told me "what have you done?" or "what did you do?"
I would use "what have you done" because the action is not unrelevant to present.