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.
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.
When Turk and Elliott are in the line at the cafeteria, you can see that Turk has two plates on his tray and Elliott has a juice box on her tray. When they turn around at the end of the line Turk has just one plate on his tray and the juice box on Elliott's tray is also gone.
When JD suggests that Dr Cox turns to Elliot for help, the metal file that Dr Cox is holding turns around between shots. In some shots we see the plain, smooth side - in others, the ridged side with a label.
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.
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."