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.
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.