Deliberate mistake: When Boo laughs repeatedly while playing hide-n-seek with Sully in the men's room, nothing happens to the electricity - no surges as with all other times she laughs. [In the audio commentary by the directors, they explained that it would've been distracting if an energy surge occurred every time Boo laughed, so they simply didn't address the issue. A reasonable course of action, but still a mistake.] (00:37:30)
Continuity mistake: After the Scare Floor shuts down at 6:00 and Sulley goes back to do Mike's paperwork, the clock reads 5:48. After he returns again to put Boo back, it clearly shows 5:48. Finally, after Randall leaves and Sulley leaves the Scare Floor for the restaurant, the clock reads 6:48. (00:22:06)
Other mistake: When Sulley and Mike take Boo into the Factory, they see all of the CDA agents. There are 3 talking to Mr. Waternoose(as we see seconds later). One of them is number 00002. When they are done, they escort Mr. Waternoose to somewhere else. However at that very second another agent comes in with a metal detector thing. His number is also 00002. (00:35:20 - 00:36:10)
Continuity mistake: At the beginning when you see the monster in the testing room from under the bed with the glowing eyes, you also see the soccer ball on the left side of the screen. This shot takes place on the side of the bed. After the monster gets scared, he backs up kicks the soccer ball, but it is now at the foot of the bed in the middle of the room. (00:02:35)
Continuity mistake: At the beginning of the film, we see Sully asleep in his bed and the alarm clock/radio on a bedside cabinet to the right. Later, when Boo climbs into Sully's bed, the clock/radio isn't there anymore. (00:04:50 - 00:32:30)
Continuity mistake: At the beginning when the monsters are at the testing room, you can see the boy in the bed seeing something opening the cabinet. He closes his eyes and opens them up again to see a sweater sticking out. But when another monster sees what he does wrong on the tape, the sweater isn't sticking out anymore. (00:03:40)
Continuity mistake: When Mike takes the toilet paper off his feet, it's lying on the floor in the hallway. But when his girlfriend comes and yells to him, it's gone.
Factual error: In the scene where Waternoose and Sully are talking, Waternoose gets himself some "coffee", which is sludgy and thick and takes quite a while to pour from the machine. Seconds later, he takes a very quick sip. Since the liquid was so thick and there was little in the cup, it would be impossible for it to pour that fast.
Continuity mistake: At the start of the workday, Randall opens the first door with the knob on the left and hinges on the right. When he comes back out, the knob is on the right and the hinges are on the left. (00:14:45)