Other mistake: In the Briefing Room, while Kirk is feeling the effects of the disease, Spock tells Scotty that he will call the restart formula in from the bridge. But just a moment later, Kirk enters the Bridge, and Spock is in the Engine Room working on the settings and formula with Scotty.
Other mistake: After Scotty makes his remarks to Spock, he raises his phaser. The sparks start up before Scotty levels his phaser.
Other mistake: In the Transporter room, as the Decontamination field is used, the shuttered lighting casts not only on Spock and Joe, but on the walls surrounding the chamber.
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.