Continuity mistake: After Spock mind melds with Nomad, Kirk hustles him out into the corridor. In the shots taken from behind Kirk, the Captain's left hand is high on Spock's shoulder. In the reverse angles, his hand is several inches lower on Spock's arm. (00:35:00)
Continuity mistake: When Kirk and Spock get to Sick Bay, the doors open to reveal Nomad coming out. But the shot of Nomad coming out is a re-used shot of it coming out of the Turbo Lift, not the Sick Bay, as the nameplate said. (00:42:10)
Continuity mistake: When Nomad initially attacks the Enterprise, Uhura appears/disappears in subsequent shots of the bridge.
Continuity mistake: When Nomad first appears on the bridge, the indicator light on Scott's communicator panel is on. A second later, it's off, and he turns it on to say his line.
Continuity mistake: As Nomad first hears Uhura's singing, it extends antennae and leaves the room. After a quick cut scene, as it turns in the corridor the antennae is retracted, then out again on the bridge.
Continuity mistake: When Scotty awakens in the sick room after being attacked by Nomad, Nurse Chapel has her hands placed on him. In the next shot, when McCoy tells Scotty to take it easy, Nurse Chapel's hands are no longer on Scotty, and in the next shot, her hands are back on him.
Continuity mistake: When the security team is escorting Nomad back to the holding area, he goes his own way. One of the team then says, "Hey Nomad!" and begins to reach for his phaser. But in the next shot, he has already got his phaser out and trained on Nomad.
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.