In the beginning of the film, there is a "picture" of Stifler's cousin's butt (the role played by 'Sean William Scott' in previous films). In the DVD release it was revealed that the picture was that of Ross Thomas' butt.
When Erik and Brandy are in the pool room, when Brandy takes her bra off, Erik hits the cue ball and tosses the pool cue. In the next two shots of Erik the cue ball is in the same spot. Then it's gone again.
When the boys are visiting Stifler in hospital, and he's telling them about the naked mile, he's holding a cup of pudding in one hand and then it swaps to the other end in the next take. This happens a number of times through out the scene.
What are the differences between the r-rated and unrated version?
A
As well as the other moves "American Pie Presents: The Naked Mile" was released in two versions within the USA: An r-rated and unrated-version. This time the differences are marginal. Scenes with display of female private parts were exchanged for more harmless ones and additionally some scenes of ejaculation were removed. A detailed comparison can be found here.