Continuity mistake: The green Alfa in the opening minutes has its side, and mirror, wiped out by a lorry. For the next 5 minutes it then drives around in perfect condition. (00:05:43)
Continuity mistake: When Kevin goes to the grocery, he buys Tide detergent. While walking home, the two bags break, but no Tide detergent falls out.
Continuity mistake: There's an electrical outlet on the wall below the window (aligned with the window shade's loop) in Sid's room near the Megadork poster, but when Sid throws Woody to the floor and raises the shade (before he scorches Woody's forehead with the magnifying glass), that outlet has vanished.
Visible crew/equipment: When Lionel returns to the jazz bar and discovers Billy Rose has been killed (framed as a suicide), you can see two people standing in the shadows to the left of Lionel as he enters the main room where the stage is located. A man is hunched over, whilst a woman is standing still wearing what looks like a dust mask. (01:32:27)
Plot hole: Isn't it rather strange that nobody outside the Howard family's small town expresses any interest in the confirmed discovery of a new human sub-species, the only one on the planet? Wouldn't it be more likely that their little backwater town would be inundated with every press and scientific organisation on earth, and that the Howard family would be the centre of the greatest publicity carnival of all time?
Factual error: The vents that Hunt and his sidekick crawl down at CIA Headquarters are standard galvanized iron box vents; they are very common in the building trade. Try walking or crawling down one - you'll make a noise like the sky is falling down. People will be able to hear you for miles. Every person in that building would know somebody crawling about in the vent system. (This error applies to dozens of films, not only this one).
Continuity mistake: When Sam is in his bedroom, after he finds the Cube sliver it falls and dramatically burns a hole through the floor into the kitchen. But Sam's bedroom is over the living room (there is nothing on the ground floor below Sam's elevated bathroom, and in the first movie Jazz hides in this open space), and the kitchen is actually located between the den and dining room, at the other end of the house. If they were to follow the actual floor plan of the house, the Cube sliver would have landed in the area of the piano in the living room, but where would the fun have been in that? (00:12:30)
Factual error: In circling over Washington Dulles, a plane would fly over several airports that they could land at with perfect communication, including Richmond, Baltimore, Andrews AFB, etc. Also, there is no communication from the airport to the plane but the plane would be in range of no fewer than 15 transmitting stations that could have relayed messages.
Factual error: The movie starts in 1985, jumps '5 years later' and then back to Sasha Luss, then '3 years earlier'. So, in her crusty apartment in an impoverished neighbourhood of 1987 Soviet Russia, Anna is filling a form on her notebook-style laptop, too modern for the era. It looks like a NEC UltraLite (considered the first notebook style laptop) which didn't even come out until 1989, let alone the likelihood of someone in the USSR having one.
Continuity mistake: When Pierce's wife is walking in her auto shop they pan down to show her red Louboutin heels, then they cut to her walking in her office, and when they show her shoes again they have a tan sole.
Continuity mistake: When they finally arrive at the bottom of the sewer, Eddie's bandage is on a different cheek. (01:59:00)
Continuity mistake: In the final fight scene on the plane between Jinx and Agent Frost, Jinx is slashed across her stomach, drawing blood. In a later scene, when Jinx and 007 are pouring diamonds over one another in the hut on the cliff, her stomach is unblemished. (02:02:25)
Continuity mistake: Right before they rob the police car, a Boeing 747 (four engines) is seen in shots of the plane coming into land. When the plane is shown from behind, it is a Boeing 767, with only two engines and fewer main landing gears. (00:30:10)