Continuity mistake: When Spock shows the others the machine which must be put "in the proximity of the Companion", in the closeup Spock's left arm is up on the machine and we see the chair opposite Spock is empty. However, in the next shot Spock's right arm is up by the machine and Kirk is sitting in that chair. (00:22:10)
Continuity mistake: The shiny gold blanket covering the dying Commissioner Hedford is tucked up to her neck in close-ups, but only reaches her upper waist in full shots. (00:36:45)
Continuity mistake: Kirk is holding the communication device out to his right from his view of the Companion and Cochran's, but the next instant shot shows Kirk holding the device close to his chest as he speaks with the Companion.
Continuity mistake: The designs of the fabric the Companion holds up to view Cochran are different from her view versus the view from Cochran's.
Continuity mistake: After landing on the planet, the interior walls of the shuttle craft or well-lit, and light green in color. As Kirk and party exit, the interior is seen to be dark and gray.
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.