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.
Continuity mistake: When Sarek enters the banquet room to take his medication, the Tellarite sitting at the table holds a glass in his right hand. In all the full shots with Sarek in the foreground, the glass switches to the Tellarite's left hand. In all the close-ups of him, it's back in his right again. (00:14:50)
Continuity mistake: During the fight with the Andorian Kirk was stabbed in his lower kidney region, he even holds his hand there to stop the bleeding. In sickbay later on, he has a bandage around his chest and McCoy says he has a punctured lung. (00:28:30)
Continuity mistake: Just before Kirk kicks his attacker for the final time during the fight in the corridor, the Andorian picks the knife up off the deck with his left hand. In the very next shot, the knife has instantly switched to his right hand. (00:28:30)
Continuity mistake: After their life threatening surgery, Spock and Sarek somehow manage to switch beds between being in surgery and recovering. (00:45:00)
Continuity mistake: In one scene the Enterprise's phasers were pink instead of blue.
Continuity mistake: An Orion spy (disguised as an Andorian) attacks Captain Kirk in the corridor on Deck 5 and plainly stabs Kirk in the back on the right side. As he staggers to his feet, Kirk first reaches to the wound with his right hand, indicating that it is, indeed, on the right side of his back. He then reaches far across his back with his left hand to touch the wound, and we see blood on the back of his hand (but not on his sleeve). So, it is visually established that the wound is on the right side of his back. But, a few moments later in SickBay, Dr. McCoy announces that Kirk's wound is a "puncture to the left lung." Then, later in the episode, Kirk his holding his left arm as though he is suffering pain on the left side.
Continuity mistake: In sick bay, close ups of Sarek show him sitting up at a 90 degree angle, but the long shots show him reclining at a 45 degree angle as the shots cut away and back.
Continuity mistake: In the reception room, Amanda's glass goes from 1/4 filled after McCoy poured more, to over 3/4 full without his adding more.
Continuity mistake: Mr. Sulu's equipment comes up to aid him at red alert, yet shortly after it is gone. (00:39:00 - 00:40:00)
Continuity mistake: Kirk's arrow strikes the Klingon in the knee. But a few shots later, the shaft is protruding from his thigh, several inches above its original position. Still later, he's holding one hand to his calf just below the knee, which isn't where the arrow was either time. (00:43:40)
Continuity mistake: When Kirk's arrow hits Kras it protrudes from his leg, but in the next wideshot as Kras screams and stumbles the arrow is quite gone from his leg, but three shots later the arrow is back in his leg while he tries to pull it out. (00:43:40)
Continuity mistake: After Maab gives Eleen back her life and forfeits his own life, when Keel throws the kleegat and hits Kras he drops the phaser in the closeup, but in the next long shot the phaser is back up in the Klingon's (stuntman) right hand. (00:45:50)
Continuity mistake: When the Klingon shoots Maab with a hand phaser, the beam is yellow as he fires, but red when it strikes Maab. (00:46:00)
Continuity mistake: The Klingon is standing on a hillside above Maab, yet when he fires his phaser, the beam streaks upward. From that angle, he wouldn't have hit anything but sky. Nevertheless, the beam somehow re-angles itself downward so that it hits and kills Maab. (00:46:05)
Continuity mistake: Before the Capellans reach him, the Klingon's body moves into a completely different position, and to a different spot on the ground, than it was in when he first fell. (00:46:10)
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.