Operation -- Annihilate! - S1-E30
Continuity mistake: When they put the satellites in orbit, Sulu announces they are in place. Then Kirk says "Energize" and the next shot shows the helmsman station and Sulu is absent - some guy in a red shirt is there instead. (00:45:30)
Operation -- Annihilate! - S1-E30
Continuity mistake: When Uhura tells Kirk that she's made contact with his private transmitter she's seated at the communications console, with the two overhead screens above her station, beside the turbo lift alcove. Yet after the contact's been broken, when she tells Kirk, "It's impossible at the moment because they stopped broadcasting," in this unusual shot facing Uhura the turbo lift alcove is not behind her - Uhura is actually seated much closer to Spock's station, note the upper section with overhead screens. Then she's properly seated at her station once again.
Continuity mistake: When Kirk confronts Spock in his quarters, Kirk asks if it's something only his planet can do for him, then Kirk uses his left hand to grab hold of Spock's arm as he drops the stylus, but in the closeup it's Kirk's right hand holding Spock's arm up, and that stylus is also back in Spock's raised hand. (00:12:25)
Continuity mistake: Spock is standing in the background with his back to the wall and his hands behind him. A few seconds later, the shot changes to him deep in the "Plak Tow", with his left shoulder touching the wall and with his hands intertwined. The next shot has him standing with his back against the wall again, hands behind his back again. The scene would have flowed nicely if they hadn't inserted the "Plak Tow" shot in between. That two second clip had been used already a few minutes earlier. (00:33:03)
Continuity mistake: Just before T'Pring calls for the challenge, there's a wide shot of her going toward the gong. Then they cut to a closeup and she is standing beside Stonn, and then she starts moving toward the gong again.
Who Mourns for Adonais? - S2-E2
Continuity mistake: Apollo's lightning bolt throws Scotty across the table and dislodges a big bunch of green grapes from the fruit bowl. They fall onto the table. But when Kirk's crew later assemble at the table, the green grapes aren't there, or in the bowl, or anywhere in the temple. They magically reappear in the bowl just after Spock gets through to Kirk on the communicator. (00:18:55 - 00:41:10)
Who Mourns for Adonais? - S2-E2
Continuity mistake: Kyle reports the landing party's whereabouts on the surface, and Spock asks, "And Apollo?" Kirk had no chance to call the ship after Apollo revealed his name - so Spock should not have known it. (00:22:10)
Who Mourns for Adonais? - S2-E2
Continuity mistake: The fruit bowl disappears from the table altogether just before the Enterprise fires on the temple. The small statue that's been there from the start vanishes as well. (00:44:25)
Who Mourns for Adonais? - S2-E2
Continuity mistake: In the original version, the giant hand is holding the Enterprise for most of the episode, but when the Enterprise fires phasers at Apollo's temple, the hand is gone.
Continuity mistake: After Spock mind melds with Nomad, Kirk hustles him out into the corridor. In the shots taken from behind Kirk, the Captain's left hand is high on Spock's shoulder. In the reverse angles, his hand is several inches lower on Spock's arm. (00:35:00)
Continuity mistake: When Kirk and Spock get to Sick Bay, the doors open to reveal Nomad coming out. But the shot of Nomad coming out is a re-used shot of it coming out of the Turbo Lift, not the Sick Bay, as the nameplate said. (00:42:10)
Continuity mistake: When Nomad initially attacks the Enterprise, Uhura appears/disappears in subsequent shots of the bridge.
Continuity mistake: When Nomad first appears on the bridge, the indicator light on Scott's communicator panel is on. A second later, it's off, and he turns it on to say his line.
Continuity mistake: As Nomad first hears Uhura's singing, it extends antennae and leaves the room. After a quick cut scene, as it turns in the corridor the antennae is retracted, then out again on the bridge.
Continuity mistake: When Scotty awakens in the sick room after being attacked by Nomad, Nurse Chapel has her hands placed on him. In the next shot, when McCoy tells Scotty to take it easy, Nurse Chapel's hands are no longer on Scotty, and in the next shot, her hands are back on him.
Continuity mistake: When the security team is escorting Nomad back to the holding area, he goes his own way. One of the team then says, "Hey Nomad!" and begins to reach for his phaser. But in the next shot, he has already got his phaser out and trained on Nomad.
Continuity mistake: When Kirk sits down to consult the computer, the big green potted plant on the shelf behind him is there in full shots and missing in close-ups. It's much too large to be completely hidden behind him: if it shows up behind his head in full shot, it should show in close-ups, too, but it doesn't. It's not there. (00:16:30)
Continuity mistake: Kirk punches the Imperial crewman that helps him in the face, but when the guy falls on the ground he's holding his side.
Continuity mistake: A subtle mistake, but when Spock is lying on the table in sick bay and recovers, the readings on the monitor are in the normal range. However Spock, as a Vulcan, produces very unusual readings on the monitors in other episodes.
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.