Revealing mistake: When Will Smith throws a rock at the escaping Edgar alien, if you watch the rock after it hits the alien, it disappears after hitting the ground.
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.
Continuity mistake: Just before the diner scene, where the two aliens are discussing the galaxy, we see the outside of the Russian restaurant. The neon sign says "haroshaya" meaning "good" all the way across the window, in the next shot inside the restaurant, the "ha", which looks like the English letters "xo", is gone and the sign is centered.
Continuity mistake: When the Bug's spaceship floats over Shea Stadium and the NY Mets outfielder sees it and gets conked on the head by the fly ball, he is wearing number 23. In a later scene, when J picks up the tabloid newspapers, the photo of the ballplayer has number 20.
Continuity mistake: When the jeweller leaves his shop, the shop window clearly shows the reflection of the parked exterminator's van. Then you see the van being driven up the cross-street as the jeweller leaves in the taxi. Then Edgar/bug parks the van, goes to the shop, and you can see the same reflection in the jewellery shop window.
Visible crew/equipment: When Tommy Lee Jones shakes the dog asking him about the galaxy, right before they exit the car, you can see the cameraman's reflection in the shiny black door frame.
Continuity mistake: When Will Smith and the other recruits are taking their written tests, the white table first appears to be situated between the second and third men from the left. When Smith goes to the table to pull it across the room, it is much further to the right of the scene.
Continuity mistake: When J is changing in to his suit, he reaches in to the locker with his right hand and pulls out a hanger with a pair of trousers and a jacket on it. His forearm is bare and he isn't wearing a watch. Seconds later when he takes the shoes out of the locker with his left hand, his forearm is now covered by the long sleeve of a white shirt and he has a silver watch on. A few seconds later when he lays the jacket over the bench, both his forearms are bare and again he isn't wearing a watch.
Revealing mistake: There is a scene where Agent J is standing on a car and shoots the "Noisy Cricket" at the fleeing Edgar. The camera shot is from inside the car and just before Agent J crashes through the windshield, you see a precut area in the glass.
Visible crew/equipment: In the scene in the beginning where Will Smith chases the alien who jumps off the bridge onto the street. Will Smith jumps from the bridge onto a tour bus, then jumps on the back of a newspaper delivery van. In the passenger side of the van is a cameraman with his back towards the windshield in order to film down the side of the van as Will Smith jumps off the van.
Other mistake: When K is searching for his wife on the computer, the zoom in highlight boxes don't match the videos.
Continuity mistake: When the countdown timer for the destruction of Earth appears on the viewscreen, you see it count down to 59:56. There is a cut to three cast members including Will Smith and Tommy Lee Jones for a brief dialogue scene. When it cuts to Will Smith walking away you can see the clock still counting down on the screen in the background. Now it is showing the time of 59:54. The aforementioned dialogue section took noticeably longer than two seconds.