Character mistake: When Jeebs is showing them his deneuralizer and it shorts out a moment, he states he's still running off the 6.0. However the computer display shows he's using the beta 0.93.
Deliberate mistake: When MIB agents exit the lift to get into the main hall of the MIB Office, the lift opens halfway up the wall and they need to go down a little platform. But when K and J return during the lockdown and face the trashcan with guns, the lift opens at floor level, so it can be conveniently peppered with bullets. (01:02:05)
Suggested correction: The building is in lockdown so it is no surprise that the lift is changed to a less flamboyant version. Even in the first scene, there are some doors there.
Visible crew/equipment: When Agent Kay is in the elevator with the little worm dudes he swings down and starts shooting at the robot. When he swings down you can see the safety harness between his legs. (01:02:50)
Continuity mistake: When Frank the dog is growling at the agent in the park his teeth are fine but later talking to Zed he is told he can have better dental. He smiles and his teeth are horrible. (00:23:50 - 00:31:10)
Continuity mistake: In the scene at the lockers in Grand Central Station, Agent Kay takes his watch, an illuminated Hamilton digital, back from the little animals living there. In one shot, Agent Jay puts an analogue watch in the locker as a replacement, but in the next shot it is the same old Hamilton digital owned by Agent K. (This is mentioned in the DVD Audio Commentary with Barry Sonnenfeld). (00:51:15)
Visible crew/equipment: When Jay enters the tent in which the small alien craft had landed we can clearly see the camera man in the golden reflection. This happens twice. (00:25:00)
Continuity mistake: When Agents Jay and Kay are in the elevator avoiding the garbage can robot who is shooting at them, watch their hands - they move from the wall to the roof ledge for support as the camera angle changes. (01:02:10)
Other mistake: About halfway through the film, there is a screw-up in the editing. After Serleena talks to the thugs, she proceeds to talk to Jarra. The next time we see her, she is interrogating Zed. Soon after, she is talking to Jarra as if she was never interrupted. (00:39:25 - 01:03:40)
Continuity mistake: When Jay is trying to tranquilize Jeff he gets hit in the head by a crossbeam which lays him back on Jeff's back. You can see that the syringe is not in his hands or his mouth, but when he sits back up he has it in his mouth again. (00:08:25)
Continuity mistake: At the beginning of the movie, when Serleena first lands on Earth, her ship crashes into the ground and creates a mound of dirt. When Harvey the dog comes over to check it out, the mound is gone. (00:04:43)
Continuity mistake: When Jay is giving Kay his favorite gun "little cricket" he is seen holding it by the lower part of the handle. The camera angle changes and he's holding it differently. The camera angle changes again and he back to holding it by the lower part of the handle. (00:31:45)
Continuity mistake: When Agent Jay and Tee are talking in the diner, a young guy passes behind Jay towards Tee, but disappears when the angle changes. (00:13:10)
Deliberate mistake: When the trashcan opens fire on the lift with Jay & Kay in, the distance and angles mean it would, at most, be able to hit up to the edges of the rear doors. When the inside of the lift is shown, the bullets have somehow managed to reach right to the edges of the lift. (01:02:15)
Continuity mistake: When Lara Flynn Boyle is holding up Tommy Lee Jones with her tentacles, in one shot you can see the tentacles coming out of her fingers, but when they show her up close, there are no tentacles coming out of her fingers. (01:04:15 - 01:06:45)
Continuity mistake: After Jay and Kay go to see Jeebs about the deneuralizer, Kay leaves and the bad aliens come crashing through the walls. Jay shoots Jeebs head off and, as it's growing back, he says he got shot "right in the pie-hole" (mouth). However he was facing away from Jay when he was shot and it was above the mouth area. (00:40:25)
Continuity mistake: In the scene where Jay is fighting with Jarra, we see the clear rubber tubes in very back of the room. After defeating all the Jarras there is only six seconds left to stop the launch. He could not make it from the back of the room to the rocket in time to stop the launch. (01:05:10)
Continuity mistake: When J and Kevin get flushed they end up in 2 cans in times square. In the long shots the cans are the same height, but in close ups, Kevin's is slightly shorter than J's. (00:35:30)
Continuity mistake: When J is trapped by the subway slime monster there are no cars on the left and a big mess is done on the curb and pavement. However, from the opposite side of the street, a frame later, the place is full of cars with no sign of the previous destruction.
Continuity mistake: When Kay shoots Jeebs' head off, him and Jay are shoulder to shoulder looking down at Kay. Jeebs' head acts like a popped balloon full of green goo, but none of it gets on Jay or his suit. (00:41:20)
Continuity mistake: When Jay is in the fight scene with Jarra and his clones, Jay jumps up two clones to get to Big Jarra, but when the camera angle changes, the Jarra clone he jumped on is gone. (01:04:35)
