Continuity mistake: The landing party beams down in daylight, but the window inside Mendez's office shows that it's night outside. In the next exterior shot, it's day again. Next shot back in the office: night. (00:00:30 - 00:05:20)
Continuity mistake: Kirk introduced Spock as "Lieutenant Commander" instead of "Commander".
Other mistake: While on Starbase 11, Kirk and McCoy watch Pike on a starbase desktop monitor as his light keeps blinking no. When Kirk is with Mendez in his office discussing the Talos IV top secret file, Piper watches Pike on the desktop monitor in the office. Then Spock uses the desktop monitor in his quarters to watch Kirk. All these consoles have the same dings and markings around their screens, which are also the same as other desktop monitors on Enterprise in the previous episode, The Corbomite Maneuver. (00:11:10)
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.