Continuity mistake: When Agent J drives to see the small, gold alien ship in the yellow tent, he steps out of his car and into a small amount of mud. His shoes already have mud around the soles and edges when he steps out. (00:24:30)
Revealing mistake: When Agent Jay is in the yellow tent with Serleena's tiny ship, the view back at HQ shows a shot from a distance behind the ship of Jay holding the communicator he's supposed to be transmitting the video from.
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)
Continuity mistake: After being flushed, the amount of water on J's chin increases in the close-ups, but decreases in the wide angles. (00:35:35)
Visible crew/equipment: When Serleena is at MIB headquarters to give her credentials, the dolly shot shows an aquarium with an alien in it on which a boom operator and a crew member walking are reflected. (00:34:04)
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.
Visible crew/equipment: When Jay is addressing the civilians in the small section of the subway car that is left after Jeff ate the rest, green screens are reflected in Will Smith's sunglasses before he neuralizes them.
Continuity mistake: At the post office, K waves his hands at J and turns around to where the employees are. When the angle changes K is waving his hands again.
Audio problem: When Jay and Frank are rolling up to the pizzeria, Jay is replying to Frank. As the car comes to a stop, and after they get out and go into the store, you hear Jay, but his lips aren't moving.
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: 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: 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: Serleena's ship lands completely perpendicular to the ground, but when the angle changes it's pointing a 2 o'clock position.
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: When they land on the roof of the launch site, Jay gets out of the passenger side, even though he and Kay switched spots after which Jay was driving/flying.
