Deliberate mistake: In one of the later episodes of season 2 Turk is seen being bored in surgery and checking the patient's wristwatch to see how long they have been operating. Patients are not allowed to wear jewelry or watches during surgery as there is a VERY high risk of infection and it might kill them.
Character mistake: JD is having problems with someone dressed in a gorilla suit, who is slightly shorter than he is. JD sees the janitor, who is considerably taller than he is, eating a banana and accuses him of being the gorilla. If the janitor were as tall as JD, maybe, but you would not confuse someone shorter than you with someone taller, regardless of costume.