The original pug from Men in Black (1997) was used to play Frank again, but since the pug was now seven years older, they used makeup to hide the gray fur around its nose.

J's line on the "driver airbag" ("Actually it came with a black dude, but he kept getting pulled over.") was improvised by Will Smith. The producers liked it so much it even made the theatrical trailer. Barry Sonnenfeld however was not happy, it was played over and over in the month of June prior to the film's release, making the joke old and tired by the time people saw it in the movie.

J tells T to "Get married. Have a bunch of kids" and then hooks him up with a waitress (played by Alexandra O'Hara). She is credited as "diner waitress". In Men in Black 3 (2012), the waitress reappears as a housewife with several kids (she is played by the same actress).

In both Men in Black (1997) and Men in Black II (2002), a tandem bicycle decorated with lights can be seen going past the pawn shop. The bicyclists are actual residents of this area of New York City.

In an interview with Will Smith and Tommy Lee Jones, Smith said: "It was great working with Frank the Pug in the first film, but since we came back he's been acting like an a-hole." Jones then said, "Yeah, Frank's had a bit of an identity crisis since the neutering."

Continuity

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 K's digital Hamilton back in the spot, replaced again by J's analog in the shots that follow.

After J and K are flushed from MIB headquarters, the tubes that they end up in are the same height in close-up but are two different heights when seen in long shot.

In most of the movie, whenever Agent J and / 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 level. 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).

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



Factual errors

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.

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

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

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.



Incorrectly regarded as goofs

When J comes out of the subway, a man walks down the left side of the stairs. J then tells 2 others that the subway is closed. The men that J lets go down the stairs are wearing black suits, and are most likely MIB Agents.

In the first movie, K says "Not bad for your second day at work, is it?". This is the same night day J neuralyses K - implying they only spend two days together as Agents. After getting flushed in the second film J 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 J! Flush me!'" - implying they spent at least a number of weeks working together, not two days. However, it's heavily implied that J's story of K wanting to be flushed every Saturday was false and intended to be more of J trying to be humorous.



Revealing mistakes

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 of the film when agent J and agent T first encounter Jeff's weed-looking hair sticking out of the sidewalk grate, agent T bends down to grab the "weed". In one shot, T is obviously tugging away at nothing at all. Evidently, the digital effects team accidentally forgot to add the "weed" (which was computer generated) to that shot.

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

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

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 we see J drop the leash so the dog can go off screen.



Miscellaneous

At 39m 35s 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 just put.

Before and after neutralization of Newton and Hailey behind J you can see a CGI ship in a poster on the ceiling rotating.



Crew or equipment visible

Green screen can be seen in J'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 J recovers from being thrown against a wall. The seam is the track for the wire harness, used when J is carried to the back of the room by a flying Jarra copy a moment later.



Errors in geography

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 you first see Ben's pizza shop, it obviously has a second floor and is a brick building. When Serleena is in the pizza shop holding up Ben, you see yellow ceiling tiles with square designs. Then in the same scene when Laura is crying in the kitchen, it shows the ceiling again 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.

Near the end when K presses the red button, you clearly see Times Square behind them. In the next shot of the car, they are seen flying through Times Square again (notice the Virgin Sign passing twice).



Plot holes

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 J and K 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.



Character error

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.

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.

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.