Continuity mistake: During the scene where the class is being warned about the dangers of being a "wait and see" type of doctor, JD imagines himself as being the only person in the auditorium. In the first shot of him alone, there is a bookbag (or something similar) sitting on a seat about three seats to JD's left. In the next shot of him, it is gone, and in the third and final shot of him alone, it is back again.
Continuity mistake: When J.D lends his nasal spray to Doug in the final scene Doug returns the spray to J.D after putting the cap back on. In the very next shot as J.D says "Don't bogart my nasal spray", J.D uses the spray without putting on the cap, and you can see the cap placed on Doug's tray.
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.