Revealing mistake: As the Enterprise passes by the camera in the opening, as Kirk does the Log entry monologue, it's easy to tell where the studio lighting was positioned.
Revealing mistake: When Spock and "good" Kirk are searching engineering for the "bad" Kirk, there is an obvious cut in the shot just before "bad" Kirk jumps down from his hiding place.
Revealing mistake: When the "pleasant" Kirk and Spock go down to the engineering level to get the "animal" Kirk, they split up and "pleasant" Kirk meets the "animal" face to face. As he steps out from behind a screen type wall, you can see that the "animal" Kirk is really Shatner's stunt double helping to fill the double role. This can also be told by the size difference when the two are close together and the shot is from behind the double.
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.