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.
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.
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)
Factual error: Gorillas are almost exclusively herbivores. They have been observed eating small insects and grubs but nothing larger. So why does Isabelle eat a rat at the beginning of the film? The serum may have turned her into a crazed killer, as it does with Sebastian, but it hasn't changed the structure of her teeth and palate, biochemistry of her digestive system and so on, all of which would be required. She might kill or torture the rat, but she'd never eat it.
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)
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?
Plot hole: How does the little girl Nina know Ferdinand's name if only the animals can communicate with each other? They're all calling him Ferdinand before she "names" him that.
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: 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: 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)