Continuity mistake: In the apartment there is a cardboard box on a table, with a strip of blue tape on it and a tube of paper sticking out of it. A few shots later another strip of blue tape suddenly appears on the box and the tube of paper has vanished. (00:02:35 - 00:03:15)Hamster
Character mistake: Early in the episode, Keith pages JD from home to the hospital. When JD arrives, he asks Keith what's the big emergency and Keith asks if he wants the patient to be prescribed unfractionated or low molecular weight heparin. JD gets angry and says that they're the exact same thing. This is in fact completely incorrect. Low molecular weight heparin is made from fragments of unfractionated heparin. They have different effects in their metabolism, half life and dose monitoring (unfractionated needs a blood test, low molecular weight doesn't). The choice between unfractionated and LMWH is an important clinical decision and should not be dismissed as "the exact same thing".
Plot hole: Season 5, episode 20 (My Lunch). One of Dr. Cox' patients needs a heart valve transplanted. Heart valves don't have to be transplanted from another person. They can be replaced by a metal valve, or the surgeon can create a new valve from a different part of the patient's body. There was no reason to wait for a donor valve when they had other options available.