In the second variation of events, just after Carla complains to Turk about not standing up for her, she goes to walk 'away' from him, but when the scene cuts to another angle, he is on the other side of her and she has to walk past him to leave. It's a re-use of the first variation of this event.
In the first variation of events, Dr. Kelso questions Carla as to why she has yet to clock out 9 minutes after her shift ended. In the second variation of events, which is supposed to have begun 10 minutes later than the first variation owing to the handshake with the Janitor, Dr. Kelso again questions Carla about why she has yet to clock out 9 minutes after her shift ends, when it should have in fact been 19 minutes.
Dr. Kelso throws a pen between JD and Dr. Cox which JD fails to catch and it lands on the floor in the open doorway behind them. JD and Dr. Cox then walk through the door without picking up the pen. The camera angle then changes to Dr. Kelso for moment then back to the doorway and the pen is gone.