Continuity: The woman in the wheelchair that Dr. Cox claims is dead is wearing glasses in some shots but not in others.
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JD: Who put this mistletoe up?
The Janitor: I did. I drove around the whole city before my 5 AM shift, just looking for that. Trying to add a little cheer. You will not ruin my Christmas. Not again. Not this year.
JD: But I've only worked here three months.
Trivia
The shot of the car driving off the bridge was actually taken from the Tom Cruise film Vanilla Sky, as mentioned in the director's commentary. See more...
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starring Donald Faison, John C. McGinley, Judy Reyes, Ken Jenkins, Neil Flynn, Sarah Chalke, Zach Braff (add more)
Updates: 
Series 5
Pilot (season 1, episode 1)
Continuity: When Elliot and J.D are going up the stairs and J.D asks if they are racing, Elliot has a watch on her left hand, then in the next shot when they are racing, the watch is gone and doesn't reappear.
Continuity: Right at the end, the shot shows Carla walking towards JD with a security guard in the background, the shot cuts to behind JD and suddenly the security guard has moved forward in position dramatically.
Continuity: When JD says it might be a penny blocking the door the Janitor says "If it's a penny in there, I'm taking you down" while placing his screwdriver on JD's shoulder. When it cuts he places it under JD's chin.
Continuity: Dr. Cox's stethoscope is hanging down more on his left side, but when he walks around to J.D. it is now hanging evenly around his neck.
Continuity: When JD is in the lift (elevator) with all the people and asks his patient if his gas is bad for the other people, the woman on the right has her arms crossed then in the next shot she has a single hand on her chest.
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