Audio problem: When Will Smith is looking at the two space ships at the MIB headquarters, if you look in the background Zed and K are there typing on the computer. But if you look closer you can tell that they're not even touching the keyboard and the sounds are just added into the movie. (01:16:00)
Audio problem: The ship is going at full speed towards the coast - making a roaring engine sound. But when it hits the coast and stops, the sound of the engines stop too. Who turned them off? (01:46:25)
Audio problem: Near the end of the film, when we see the Queen's new mutation, the scene opens up by showing all the scientists attached to the wall. Dr. Gediman is rambling on and on about the Queen's 'perfect' mutation. However, it is quite clear he isn't saying any of the words. In fact, from the way his mouth moves, it looks like he's literally saying 'blah blah blah, blah blah blah'. (01:27:05)
Audio problem: When the troops are lined up on the fort's wall near the end preparing for the waves of bugs, Lt. Rasczak is walking at a fast pace behind them and shouts something before aiming his gun. Before he aims his gun, he is seen shouting the same thing as he walks past them, but there's no sound coming out of his mouth. (01:29:25)
Audio problem: When Karl is trying to push himself on Jamie, you can hear her screaming when the shot is outside the car, and the screaming continues when the shot's showing both of them, but she isn't screaming.
Audio problem: Near the end of the film, Joe's girlfriend suggests that he stays as Orgazmo - her lips don't match what she is saying.
Audio problem: When the stewardess is telling the people that she's putting on the sleep regulator, they show a different shot, and you see in the background she's mouthing words that don't match up. (01:15:25)
Audio problem: When the police and reporters are outside the warehouse where the dinosaur attack happened, Captain. Polaris communicates with other cops by radio. Strangely enough, his own voice, and the voice of the bald cop beside him also sound mechanical, with the crackling quality you hear over radios, even though they are on screen and should be heard normally. This even goes on when they are talking to each other, without using the radios.