Plot hole: When the police chief asks Joe 'where's the briefcase they were telling me about?' Joe tells him to look in the back seat of the white BMW. There are a couple of problems with this. First, the police chief is looking for a case with a bomb in it, because he received a phone call from the guy who had his BMW stolen. Even if he knew about the money, which is unlikely, the police chief has no way of knowing that the case he is about to open is not a bomb, since no-one saw Marcone steal the case with the bomb in it. Yet he opens it without calling the bomb squad. Second, Joe saw Jimmy put the case with the bomb in the back seat, so why doesn't he warn the police chief about it?
Plot hole: Marcone goes out into the parking lot, notices the white BMW, and then proceeds to shoot out the rear passenger window. Two problems with this scene, firstly, the front window is now perfectly intact when previously it was shot at during the limo chase, and secondly, Willis' character didn't even lock the car up, Marcones shooting of the window makes little sense with people around, which notably don't react to the shots at all.