There is a line in the first Monsters, Inc. (2001) where Mike says that Sully has been jealous of his looks since the fourth grade. Since this movie was going to show Mike and Sully meeting in college, it obviously contradicts that line. Director Dan Scanlon admitted that there was some conflict behind that and even had one treatment show Sully and Mike meeting in the fourth grade then skipping ahead to their university years. Pete Docter (director of the first Monsters, Inc.) and John Lasseter personally told Scanlon that they loved that he was honoring that one line said in the movie, but he "...had to do what was best for the story". As a result, the line was put aside and Sully and Mike would be shown meeting in university. As a joke, Scanlon said that Mikes line in the first movie is "an old monster expression."
Mike's parents were originally planned to be included in the story. They would drop Mike off for his first day at Monsters University. However, director Dan Scanlon decided to drop them from the finished film to make Mike seem just that much more vulnerable.
In the sequence where Mike and Sully end up in a human summer camp near the end of the movie, the child who comes out of the bathroom before Mike is about to leave roars at him. The roar is a sound recording used from Monsters, Inc. (2001) for the character, Boo.
The School of Scaring building is a visual homage to the famous Lovecraftian monster, Cthulhu. The green central dome is clearly designed in the shape of a head (with skylights placed strategically as eyes) and the columns flanking the main entrance (which itself is lined with teeth) bear a strong resemblance to Cthulhu's mouth-tentacles.
When Sully enters Mike & Randall's room with Fear Tech's pig, a motivational poster can be seen above Randall's bed that reads "Winds of Change: Shh... Can you hear them?". This is a reference to a line Randall says to Mike in the locker room during Monster's Inc.
John Ratzenberger makes his traditional Pixar film appearance, reprising his role as Yeti (a.k.a. The Abonimable Snowman) from Monsters, Inc. (2001). Yeti's job in the Monsters, Inc. mailroom is a nod to John's famous role as postman Cliff Clavin in Cheers (1982). Yeti warns Mike and Sully that tampering with the mail is punishable by exile to the human world, foreshadowing his exile in Monsters, Inc.
Early drafts included Mike and Sulley in grade school together (to respect the "fourth grade" quote in Monsters Inc.) and the characters of Celia, Fungus and Waternoose (recast as Kelsey Grammer) making appearances. Grammer's cameo was cut from the film; Waternoose appears only in a photograph.
The Monsters University campus is based largely on the University of California at Berkeley campus, which is very close to Pixar's headquarters in Emeryville, CA. The Monsters University gate is based on UC Berkeley's famous Sather Gate, and the clock tower in the film is based on Berkeley's Campanille clock tower. (UC Berkeley also carries the 510 area code, seen in the film.)
Celia and Mr. Waternoose actually "appear" in the movie. In the closing portion there's a note from Celia in Mike's locker asking her to call him. Also, there's a photograph showing Mr. Waternoose a few seconds after.