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".
Character mistake: Throughout the series, JD and Turk are shown to be major sitcom geeks. At one point in the episode, JD says to Turk he Marcia Brady'd his ass, and explains what it means. Turk responds along the lines of "Yea, I know. 'Marcia Gets Creamed' Season 5 episode 3. Don't ever question me about The Bunch!" 'Marcia Gets Creamed' is season 5 episode 10. Episode 3 is 'The Elopement'. Not a mistake a couple of geeks would make.
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.
Character mistake: When Elliot asks Kelso if there is a special way to communicate with the nurses. Kelso grabs Elliot by the arm and his hand being placed on her sleeve and pull her to the side while still holding her arm, when the camera angels changes from the close-up his hand placement is lower and not on Elliot's sleeve but on her skin.