Continuity mistake: The woman in the wheelchair that Dr. Cox claims is dead is wearing glasses in some shots but not in others.
Jeff Swanson
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
My Best Friend's Mistake - S1-E3
Continuity mistake: In the apartment, when they decide to watch "Fletch", there is a yellow cushion under J.D.'s right arm, sitting on the sofa. But it disappears between shots. (00:05:50)
Hamster 
My Journey - S3-E2
Revealing mistake: When Elliot is splashed by the dolphin, if you watch carefully you can see her hair is already wet.
Shay
My Best Friend's Mistake - S1-E3
Visible crew/equipment: In the scene where JD and Elliot are treating a patient and JD says "It's the closest thing I had to a date recently" the microphone pops into screen from above at least two times.
Mortug
Continuity mistake: As Kelso goes rolling by in the hall with the wheels on his shoes, you can see they are actually skates and the wheels are black. When he asks who put the tiny wheels on his shoes, the shoes are now normal and the wheels are white.
Lummie 
My Half-Acre - S5-E9
Continuity mistake: Season 5-9, Episode: My Half-Acre. While Cox and Carla are telling Mrs Wilk about her treatment, the cardigan she is wearing is completely unbuttoned. When the camera goes for a closeup of her face, the cardigan is now buttoned right up to her neck.
Lummie 
Continuity mistake: 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. (00:21:40)
bytemyshineymetalass
My Best Friend's Mistake - S1-E3
Continuity mistake: When Dr.Cox is Talking to Elliot before she leaves the room her name tag flips over and back again. (00:17:20)
bytemyshineymetalass
My Best Friend's Mistake - S1-E3
Continuity mistake: Dr. Cox throws his white coat on the table and sits down, when he starts talking to Elliot the coat is now missing from the table. (00:16:40)
bytemyshineymetalass
Continuity mistake: Season 5-19, Episode: His Story III. While Carla and Turk are lying in bed at the start both of them keep changing positions between shots. Turk's left arm and hand also keep changing position between shots.
Lummie 
Continuity mistake: When Eliott is lying on the couch talking to JD way her stethoscope changes position between shots.
Cybermoose
My Bed Banter & Beyond - S1-E15
Continuity mistake: When Todd is listening at the closet door, and Laverne walks past, Laverne's stethoscope goes between shots from lying flat down by her neck to draped over to the right side.
pinkwafer
Continuity mistake: When Elliot is unpacking her books at the apartment, she places a brown book on top of the pile next to her. In the next shot, there is a green book on top of the pile.
pinkwafer
Their Story - S6-E17
Continuity mistake: When Turk is talking to someone about the teenager getting breast implants, in the first shot you can see he is talking to someone in a a blue shirt with a stethoscope - i.e. JD. However after this shot, JD has vanished and the conversation is suddenly with Todd.
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.
Lummie 
Answer: Dan was drinking beer and Cox feared that Dan might get so intoxicated he would fall asleep and drown in the tub.
Mortug