Deliberate mistake: Gandu Three Echo, the clone who hits the screen showing the first lottery winner in the movie, complains that he has been around for 7 years and never won the lottery. However, McCord explains later in the movie that the last name tells how old the clones are. Lincoln Six Echo is 3 years old because he is in the Echo generation, and the Delta generation (Jordan Two Delta) is 4 years old. Going backwards, this would make Charlies 5 years old, Bravos 6 years old, and Alphas 7 years old. Gandu Three Echo should have really been Gandu Three Alpha. (00:05:55)
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. (01:16:00)
Continuity mistake: When Lando says "Go on, you pirate" his entire outfit is reversed - his shoulder holster strap goes the other way, and his rank insignia changes side too. (00:50:00)
Character mistake: When Harley asks Tony what the light is coming from his chest, Tony responds "an electromagnet." Harley replies "What does it power?" An electromagnet is not a source of power. The arc reactor is the power source which powers both the electromagnet (to keep Tony safe from the shrapnel near his heart) and the Iron Man suit. (00:43:25)
Audio problem: Anthony Hopkins is in his car with Cogman, discussing Pangea the super continent over the phone with John Turturro. There are two instances in this scene in which Anthony Hopkins' voice has been dubbed over by a different actor that does not sound like him. Anthony Hopkins first says "That's Pangea. The super continent." The scene then flashes back to the round table and the dubbed voice attempting to sound like Hopkins says "It's the same shape on the round table." The dubbed voice is heard again when he says "Genius", before reverting back to Anthony Hopkins immediately after when he says "Stonehenge."
Revealing mistake: Throughout the film, the base station radio is not connected to an antenna. In many lengthy shots of the back of the radio we can see the power cord trailing out the back of the unit, but there is nothing plugged in to the antenna socket. This is especially annoying because base station radio problems are a key plot point.
Continuity mistake: After defeating Fulton Balcus, Sean removes the armor and has no clothes on. As Sean and Mizky leave, Sean is wearing sneakers. Mizky only brought him a shirt to wear.
Factual error: When they first pick up the Mona Lisa, they show the back. There you can see a canvas sheet over a wooden framework. However, the Mona Lisa is painted directly onto wood, no canvas at all. The scan they run even says it's painted onto wood, despite visual evidence to the contrary. (00:06:35)
Plot hole: The first time they communicate with the "entity" in the spaceship, they find a correspondence between numbers sent by the entity and letters of the alphabet. The entity presents itself as "Jerry". Later on, the entity tells Dustin Hoffman, "Stop calling me Jerry" - and then Dustin Hoffman realizes that the number-letter correspondence was wrong, and the actual name of the entity was "Harry". But if that is true, how could they have communicated without problems before? The very first word that the entity used was "hello", which would have to be displayed wrong, since it begins with an "h" and has an "e".
Continuity mistake: At the start of the movie when the gun store is being robbed, one of them fires a portable rocket launcher at the police car, causing it to roll over and spin. As it comes to a stop just outside the store, it's visible that the driver's side window has been blown out, and the vehicle interior is visible, however when the same guy prepares to fire the bazooka to finish it off, the window has returned and is completely intact.
Character mistake: In the scene where Steve and Josie prepare to leave to fight the giant robot at the beginning of the movie, Steve tells Will "Oh, Will, a reminder: a lot of the kids at Sky High will only have one super hero parent, not two." When he says "one super hero parent", he holds up two fingers. When he says "not two", he holds up only one finger.