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.
Continuity mistake: While J.D. and Carla are visiting Mrs Wilks near the start she has a tray of food and a bit of paper next to the tray in front of her. In shots of J.D. and Carla the table in front of Mrs Wilks where the food was is completely clear and the food and paper keep reappearing between shots.
Plot hole: In the season 5 episode "My Fallen Idol", it is a key plot point that Turk has a hard time hugging guys. However in the Season 3 episode "My American Girl" Turk openly gives another surgeon a hug after J.D. makes fun of him. It is not possible for him to have changed because it shows that even before they became doctors, Turk would not hug J.D.
Continuity mistake: When J.D. walks up to the table where his interns are sitting, Keith and Rex are fighting with their table knives and have them crossed. The shot switches to a view from the other end of the table and suddenly Rex's knife is on the table and he is facing J.D. but Keith's knife is up in the air as if he was still fighting with Rex. There is not enough time for Rex to put his knife down and turn to face J.D.
Continuity mistake: Season 5-24, Episode: My Transition (1). The first time we see J.D. and the flyer about his deck, the flyer has a picture of J.D. looking straight ahead smiling and the writing on it reads "Old? Gay? Like Decks?" After J.D. rips the flyer off and shows it to the janitor, the picture of J.D. has changed to him giving a thumbs up and the writing has also changed to "Come and Chill at my big gay deck."
Continuity mistake: After J.D.and Julie take their picture with the old people masks and have taken them off, there are a lot of pieces from the mask still on their face. When J.D. has finished his small speech you can most of the bits from both of their faces has disappeared, with J.D's more noticeable than Julie's.
Continuity mistake: In the intro, JD comes running back into the shot after trying to change out of the same exact outfit Dr Cox is wearing. JD has the "Baby Gap" TShirt stuck & wrapped around his head turban style. The shot switches to over his shoulder and the shirt is now loose, like a towel wrapped around his head.