While J is talking to Z from the park, J closes his communicator, but Z can still see J on his screen.
When Agent K removes his digital Hamilton from the clock tower in the Grand Central Station locker, Agent J replaces it with the new Hamilton Ventura Chronograph. The next shot shows K's digital Hamilton back in the spot.
Agent J is holding onto a thin leash when he and Agent K go with the dog into MIB headquarters. Once they're inside and the lift drops to the floor we see J drop the leash so the dog can go off screen.
The movie takes place in July 2002, and Agent K sees the Orion constellation. Orion is not visible in the northern hemisphere in July.
When Agent K is fighting a ball-chinnian in Jack Jeebs' basement, the rubber mask material at the base of the face mask (right at the top of the scarf/sweater he is wearing) is exposed as he pulls down the scarf/collar.
In the beginning of the film when agent J and agent T first encounter Jeff's weed-looking hair sticking out of the sidewalk grate, agent T bends down to grab the "weed". In one shot, T is obviously tugging away at nothing at all.
In the two exterior shots of the diner, the same extras walk into the scene from the same directions. These two scenes in the movie are supposed to be hours apart.
When Serleena's ship is in the yellow containment tent, as Jay leans over to look closer the camera crew can be seen in the reflection.
When we first see Serleena's ship, we see Jay reflected on the ship. In the reflection we see him using the communicator and talking to Zed (with one hand up to his ear) which doesn't happen until a few shots later.
During Agent J's fight against Jarra, a seam is visible in the ceiling after J recovers from being thrown against a wall. The seam is the track for the wire harness, used when J is carried to the back of the room by a flying Jarra copy a moment later.
Serleena's hairstyle changes throughout the movie (Barry Sonnenfeld admitted this was a problem because of the humidity during filming).
After J and K are flushed from MIB headquarters, the tubes that they end up in are the same height in close-up but are two different heights when seen in long shot.
When J is talking to "mail man-K" in K's own car, clouds appear in the background between shots.
Scrad just disappears when J's fighting the aliens in Jeeb's basement. There is no explanation or scene that shows what happened to him .
After they are flushed in the beginning, J and K are wet, but when they get into the car they are suddenly dry without any explanation.
When the giant worm eats Serleena's flying ship in the subway, J is driving, but when they land on the rooftop K is driving.
Near the end when K presses the red button, you clearly see Times Square behind them. In the next shot of the car, they are seen flying through Times Square again (notice the Virgin Sign passing twice).
When Laura is playing twister with the wormboys in their apartment, she is supposedly holding herself up with one arm in "crab position." You can clearly see the legs of the support upon which she is reclining.
Serleena wrong answers " Yes, they're very sensitive about the Green house Effect" to a character taking the Earth's Ozone layer, even though the Green house effect is due to too much Green house gases, not Ozone depletion.