When J.D. is brushing his teeth and finds his brother is back in the bath tub and screams he has foamy lips from the tooth paste. However, when the shot cuts his lips are relatively clean again.
When Ted pulls his ice cream biscuit out of the trash and begins picking at it the amount and shape of what has been removed alters from shot to shot.
The Dido CD that Dan buys for Elliot is "Life for Rent". However, the song that J.D. sings along with is "Thank You", which is not on "Life for Rent", but instead on "No Angel".
During the scene where Dr. Clock is whistling and it begins to catch on, you can see that it was dubbed over because Heather Graham stops whistling and smiles for a second while the whistle song is still heard.