Other mistake: Spock records a log entry as the "second officer". It appears they got "first officer" confused with "second in command." (00:36:15)
Other mistake: On some VHS editions of this episode, the back cover features a picture of what appears to be both good and evil Kirk sitting at a table, however this never happens anywhere in the episode. That picture is actually from the episode "What Are Little Girls Made Of?"
Answer: Kirk was getting his physical and Dr. McCoy probably turned off communications, because if he hadn't, Kirk would have left and headed straight for the bridge, leaving McCoy irritated.