Continuity mistake: When JD tells Carla and Turk that he and Elliot had sex in the kitchen, Elliot is shocked and says "How could you possibly think it's an appropriate conversation for work?". It cuts to JD lifting his hand up and about to answer when it cuts, but now his hand is down.
Continuity mistake: When Turk and Elliott are in the line at the cafeteria, you can see that Turk has two plates on his tray and Elliott has a juice box on her tray. When they turn around at the end of the line Turk has just one plate on his tray and the juice box on Elliott's tray is also gone.
Continuity mistake: After JD has done the "Eliott got some booty" song they both walk through a door, a patient in a red dressing gown then walks past. He wasn't there before they started walking and wouldn't have had been able to get there in that amount of time.
Continuity mistake: As Dr Cox is talking to J.D. towards the end of the episode and telling him that he won't let him treat the patient he traded, Dr Cox is putting on his white overcoat. If you look at his collar on the right side it is a little crumpled and not quite straight. The next shot we see over his shoulder and the collar has straightened out. The following shot it returns back to being crumpled up a bit.
Continuity mistake: When JD's Dad arrives at the apartment, and sits down to drink a beer, from straight on his jacket is open and his tie is draped to the right. When the shot cuts to a view from the side, his jacket is now open much less, and the tie hangs straight down his shirt.
Continuity mistake: When Kelso gives Cox the rounds and Cox is surprised, he starts spanking himself with the clipboard. Notice the two women about to walk past Cox. One is in a red top, one in pink. The next shot they are passing the doors, which is well ahead of Cox. The following shot they are about to pass Cox again.