Patzer

When Agent K removes his digital Hamilton from the clock tower in the Grand Central Station locker, Agent J replaces it with the new Hamilton Ventura Chronograph. The next shot shows Kay's digital Hamilton back in the spot, replaced again by Jay's analog in the shots that follow.

In most of the movie, whenever Agent J or Agent K use the lift, they are seen being lowered down from a platform from where the lift opens to the ground of MIB headquarters. But near the end, when both agents plus the worms use the lift to fight Serleena, the lift stops at the level of MIB headquarters, with no platform having to be used to lower the agents to the same level.

Serleena's hairstyle changes throughout the movie (Barry Sonnenfeld admitted this was a problem because of the humidity during filming).

After Jay and Kay are flushed from MIB headquarters, the tubes that they end up in are the same height in closeup but are two different heights when seen in long shot.

When Frank is hiding in the dead tricrainaslov, the tentacles on the right side are crossed. However, when Jay zooms in, the tentacles are now uncrossed.

Code 101 Lockdown requires MIB Headquarters to be pressurized. When Agent J blows a hole in the entrance, everything (hot dogs, umbrella, etc.) blows into the building. Most people think of pressurization as adding pressure, but negative pressurization, which creates a partial vacuum and so would suck in outside air, is also possible. It's used primarily to prevent pathogens or toxic gasses (both of which are probably present somewhere in MIB headquarters) from escaping into the general atmosphere. It's technically incorrect to refer to it simply as 'pressurization', but it's used colloquially to refer to negative pressurization by those who use it. However, the correct term for negative pressurization is a vacuum. This is basic terminology designed to prevent confusing the two conditions and would be the terminology used by a top secret government organization.

When Serleena sticks her tentacles into Scrad's ears to pop out of his nostrils, it's potentially possible for his alien anatomy. When she sticks her tentacle tongue about 6 inches into Kay's ear (judging from the contrasting pattern on the tentacle), it should have shattered his very human eardrum.

The post office worker walking down the street with the tail coming out of his pant leg would not be delivering mail after sundown.

The Ballchinnian should more properly be called a Chinballian; he has balls on his chin, not chins on his balls.

Laura was never mentioned to have been trained in politics and has had a relatively normal middle class human life. Sending her back the Zartha as her mother's successor to the throne isn't such a bright idea in the long run. Plus she will pretty much want to abdicate the throne almost immediately after ditching her bracelet; which was the bomb that would have destroyed the Earth.

But as she was never seen in the next movie, it's likely she was forced to be around solely to continue the bloodline.

When Jay comes out of the subway, a man walks down the left side of the stairs. Jay then tells 2 others that the subway is closed. The man that Jay let go down the stairs is wearing a black suit and most likely is a MIB Agent.

In Men in Black (1997), Kay says "Not bad for your second day at work, is it?" This is the same day Jay neuralyses Kay - implying they spend only two days together as Agents.

After getting flushed in this film, Jay says "Yeah, man, back when you was an Agent, you used to love getting flushed! Yeah, every Saturday night you... you'd be like 'Flush me, Jay! Flush me!'" - implying they spent at least a number of weeks working together, not two days.

However, it's heavily implied that Jay's story of Kay wanting to be flushed every Saturday was false and intended to be more of Jay trying to be humorous.

When Agent K rips the cap off of the Pineal Eye, the rubber prosthetic with the 3rd eye can be seen to jiggle.

While Jay is talking to Zed from the park, Jay closes his communicator, but Zed can still see Jay on his screen.

In the two exterior shots of the diner, the same extras walk into the scene from the same directions. These two scenes in the movie are supposed to be hours apart.

In the beginning when Agent J and Agent Tee first encounter Jeff's weed-looking hair sticking out of the sidewalk grate, Agent Tee bends down to grab the "weed". In one shot, Agent Tee is obviously tugging away at nothing at all. Evidently, the digital effects team forgot to add the "weed" (which was computer generated) to that shot.

Agent J is holding onto a thin leash when he and Agent K go with Frank into MIB headquarters. Once they're inside and the lift drops to the floor, J can be seen dropping the leash so the dog can go off screen.

(at around 39 mins) The two characters are supposed to be looking over a body. They are just getting lower in the frame. If they were really looking over something to camera, the necklace on the right would hang forward instead of staying put.

Green screen can be seen in Jay's sunglasses when he is talking to the people in the Subway.

When Serleena's ship is in the yellow containment tent, as Jay leans over to look closer the camera crew can be seen in the reflection.

During Agent J's fight against Jarra, a seam is visible in the ceiling after Jay recovers from being thrown against a wall. The seam is the track for the wire harness, used when Jay is carried to the back of the room by a flying Jarra copy a moment later.

The movie takes place in July 2002, and Agent K sees the Orion constellation. Orion isn't visible from either hemisphere in July except for Antarctica south of the Antarctic Circle.

When Ben's pizza shop is first seen, it obviously has a second floor and is a brick building. When Serleena is in the pizza shop holding up Ben, yellow ceiling tiles with square designs are seen. Then, in the same scene when Laura is crying in the kitchen, it again shows the ceiling but with a sky window, and the tiles around it are smaller squares, ceramic and tan in color.

The movie depicts the 81st Street and Central Park West subway stop as stopping for the A and C lines and depicts platforms being on both sides of the tracks. The real stop is for the B and C lines (not A) and only has platforms on one side.

Scrad (Johnny Knoxville) disappears from the film when Jay is fighting the aliens in Jeebs' basement. He is never mentioned again, and there is no explanation or scene that shows what happened to him. Serleena later orders Scrad (who is off-screen) to get Laura who is hiding in the worms' apartment. When Jay and Kay arrive at the apartment, the worms tell them a dumb two-headed guy took Laura. He does not appear in the big fight when Kay comes to Jay's rescue.

Serleena saved Earth. If the Light Of Zartha was not taken off Earth by a certain time, it - and Earth - will be destroyed. Only Ben knew about the Light, and he didn't seem to be doing anything about removing it from Earth. Zed thought the Light was gone long ago. K had his memory wiped. If Serleena hadn't shown up, and Ben kept on doing nothing to remove the Light, the Earth would've been destroyed.

At the Post Office, all the mail being sorted and placed in the Post Office Boxes is being done by people wearing Postal Carrier Uniforms. Such work would be completed by Postal Clerks, who have a completely different uniform shirt.

Jarra says "They're very touchy about this global warming thing" to Serleena regarding taking the Earth's ozone layer, even though global warming is due to too much greenhouse gas, not ozone depletion.

When K first arrives at HQ, a suck-up offers to fetch him a cup of coffee. He replies, "Black, two sugars."

In the first film, when K takes Det. Edward's to the breakroom, K complains about only having the powdered cream.

While driving, Jay asks Kay "didn't your mother ever give you a Gameboy?" First, the controller is a PlayStation controller, which looks nothing like a Gameboy. Second, when Gameboy first came out, Kay would've already been a full-grown adult.