Plot hole: In this film, the yeti is Sulley and Mike's co-worker in the Monsters, Inc. mailroom. But in Monsters, Inc., when Sulley and Mike are banished, they apparently don't recognise him.
Continuity mistake: In the scene when Mike is at the school door lab. When he swipes the access card the door swings out. But when the campus police try to get in it is blocked from the inside, indicating the door opens inwards.
Suggested correction: If you look carefully, you will see, that those are actually two different doors, which even have hinges on different sides. There's some space between them in the entrance to the lab, it can be seen just before Mike enters.
Continuity mistake: In what is supposed to be a time-lapse scene, we see the Monsters University campus as nighttime ends and the sun rises. The shadows of the trees and buildings never change position as the sun gets higher in the sky.
Other mistake: Towards the beginning of the film, the teacher counts 19 students then says one is missing, implying there are 20 (including Mike) However, Mike ends up being paired with the teacher, despite there being an even number of students and therefore everyone should have a partner.
Continuity mistake: When Sully first pulls the folder out for the child he is supposed to be scaring during the last scare game against Randal, the girl's fear is first listed as "Thunder and Dogs." But upon full zoom in and focus, it says Thunder and Lions.
Deliberate mistake: In Monsters, Inc., when Mike and Sulley walked through Monstropolis to go to the company, Mike said to Sulley "You've been jealous of my good looks since the fourth grade". In this film, we're told Mike and Sulley met in college. [In the commentary, director Dan Scanlon explained that there was a lengthy scene that would have followed Mike and Sully throughout their years in elementary school, but it would have slowed the pace of the film and would have reduced the impact of their rivalry. Rather than spend a lot of time on a back story, Scanlon decided to have Mike and Sully meet in college, even though this was inaccurate.]
Continuity mistake: At the start of the movie Mike is on the second to last step, but in the next shot he is on the last. (00:05:15)
Plot hole: During the final scare event, Mike gets a perfect score because Sully broke the simulator to allow the 6th scarer to get a perfect score no matter what. After the contest, the simulation resets and Mike pretends to scare the child in the simulator and it registers a perfect score on the scoreboard for the 6th scarer when it should really have registered a score for the 1st scarer, because the simulator had been reset.
Continuity mistake: When Mike and Sully move into their bedroom at the fraternity house, the door opens inwards. When they fall through the doorway, it opens outward.