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)
Continuity mistake: In the scene where Agent Jay is looking at MIB HQ and sees the dead alien with tentacles, he sees something (Frank). He tells the computer to zoom in and when it does the tentacle on the right hand side half way up the screen changes shape and position. (00:36:40)
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 Jeebs is about to start the deneuralizer, watch the left part of the chain around the computer screen; Sometimes a tip of the screen is visible, others not. This changes back and forth. (00:40:10)
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 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)
Factual error: When Agent Kay looks up, after he is "deneuralyzed" he sees Orion in the sky. They're in NYC...you can't see the Evening Star, even in the middle of the night. There is no way that Kay could see a perfectly clear, and detailed constellation, complete with stars that can't even be seen in rural areas. (00:42:00)
Continuity mistake: At Jeebs' basement, when Scrad comes to talk to J, J's tie swaps back and forth between tight and loose. (00:42:25)
Continuity mistake: At Jeebs' basement, an alien lifts up J, placing his hand on Jay's right shoulder. When the angle changes, the hand is on the left shoulder. (00:43:00)
Continuity mistake: At Jeebs' basement, an alien launches J away and he lands facing to the left. A frame later his head is facing to the right. Also, his arms have changed positions. (00:43:00)
Continuity mistake: Right after Zed kicks Serleena in the face a few times, you see Serleena tripping him with the vines from her fingers and he lands on his side. The camera angle changes and he is now seen laying flat on his back. (00:44:40)
Continuity mistake: In the scene where Serleena confronts Zed in his office, look closely at her hands. Immediately after releasing Zed from her tentacles, her left hand now holds a box of Burger King fries, which disappear from shot to shot. This is most evident when she picks up the cellular phone, placing both empty hands on the desk first. (00:45:35)
Visible crew/equipment: When Serleena kicks Z and sends him flying, the person flying and doing all the flips and jumps for all the scene is a very obvious stunt: Thinner built, much younger and with longer hair. (00:46:25)
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)
Factual error: Grand Central Terminal has no lockers in the main concourse area. (00:52:40)
Continuity mistake: When Kay and Jay are watching the movie about the light, Kay starts to remember the real story and cries. The shot later, his is cheek is dry. (00:56:55)
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 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)
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)
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)
