Continuity mistake: When Kirk gives the order to Scott for transport, Spock lies in a diagonal position with the yellow spores on his chest with McCoy kneeling by him. After the cut to Scott on the bridge, Spock is lying with his head towards the camera, his chest is clean, and McCoy standing about six feet to Kirk's right. All much too quickly to be normal.
Continuity mistake: Throughout the entire episode the planet's sky is red, yet during the scenes where the clouds come and lightning strikes, it becomes obvious that they simply used stock footage of Earth's clouds, since the sky is blue. (00:11:50)
Visible crew/equipment: When Vaal is not fed and he starts spewing smoke everywhere, you can see a volcano type firework going off just inside his mouth. (00:43:55)
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.