Eddie Kaye Thomas was laughing so hard at Seann William Scott's antics during the lesbian scene that he had to be cut out of a lot of the shots. This is why these scenes contain a lot of shots of just Stifler and Jim, even though Finch is supposed to be standing right next to them.
Seann William Scott improvised some of his dialogue, this can be observed by his cast mate's reactions in some scenes, such as when he tells Jessica he wants to know how many women she has slept with that year - Natasha Lyonne's amused reaction is genuine, she isn't acting.
In the scene when Alyson Hannigan (Michelle) is "breaking up" with Jim, her hair is styled differently than normal. This is because she was shooting an episode of Buffy the Vampire Slayer (1997) and she ran over to the set during a break.
The movie originally included scenes featuring Stifler's dad (played by Chris Penn). These were removed after negative reaction in test screenings. Also missing from the theatrical release is a scene showing the band camp leader with a rash around his mouth, the morning after having played the trumpet that was inserted into Jim's ass.
Adam Herz, the writer of this film, wrote the screenplay with numerous references to the University of Michigan (his own alma mater). He also included Michigan's fight song, "Hail to the Victors", in the movie. However, the university did not approve use of its name, due to the adult nature of the film. Herz had to omit any reference to the school.