Visible crew/equipment: When K and J talk to Newton, a lighting screen is reflected in his glasses.
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.
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)
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 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: 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: 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)
Continuity mistake: During the fight scene with Jarra, Jay is dropped into the center of some large plastic tubing, but when the camera cuts to a closer shot, Jay is now seen at the edge of the plastic tubing. (01:05:15)
Continuity mistake: When Jay and Kay make their visit to Jeebs, Jay is talking to Jeebs and you see Jeebs making a statement about how his business is 'banging' and when he see Kay walk in, he points both his hands at him. The camera angle changes and Jeebes is now seen with only one hand pointing at Kay. (00:36:15)
Other mistake: In the opening scene when Sarleena takes the Vic Secret model's appearance the tentacles are just completing her face when the guy grabs her. He had to have seen the tentacles "building" her as he was walking up to her. (00:05:50)
Continuity mistake: When Agent Kay empties his guns shooting at the trashcan robot in the elevator, he throws down his guns and swings back to the roof of the elevator. When the robot moves into the elevator, the guns are nowhere to be seen. (01:03:00)
Continuity mistake: Before the alien transforms into a woman it flips the pages of magazine located inches away. When the alien starts to transform the magazine disappears. (00:05:10)