Continuity mistake: Kirk and the others are beamed down to the planet, and when the Enterprise crew are led into Mudd's throne room by two Alice androids (the Alice series are 500 identical androids) they are wearing the usual metallic, backless, kitten heel slip-ons, but in the next shot android Alice at the left is now wearing altogether different shoes - cream color with ankle-straps. (00:09:30)
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: Kirk and McCoy are in the Exeter's engineering section when Kirk uses the intercom to ask if anyone is aboard. Several shots of the deserted ship follow as his voice echoes off the walls, including one of engineering - with Kirk and McCoy suddenly, mysteriously absent. (00:03:45)
The Trouble With Tribbles - S2-E15
Continuity mistake: The tribble-inundated Kirk is holding one of the small fur balls in both hands in some shots, but when the camera angle changes, that tribble vanishes and his hands are no longer even close together. (00:40:40)
Continuity mistake: When Nomad initially attacks the Enterprise, Uhura appears/disappears in subsequent shots of the bridge.
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)
Continuity mistake: When the giant cat breaks down the cell door, Korob falls beneath it face down with his head toward the door. In the very next shot, he's in a completely different position - face up with his feet toward the door. (00:43:30)
Continuity mistake: Korob uses his wand to put a feast on the table and light the candles. Only, in the very next, close-up shot of him, the feast is gone and the candles are unlit again. Next wide shot, everything is back. (00:20:00)
Continuity mistake: Isis is an all-black cat, but in a few shots, her "stunt double" with white paws can be spotted. The cat lying on the floor of the transporter room when Gary Seven beams aboard is a white-pawed double.
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: At the end, the flag is brought in, and Kirk stands up - but in the next close-up of him, he's sitting down again. Next full shot, he's standing once more. (00:36:25)
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 Isis meows and enters the inner office, the door is open several inches and the lights inside the room are on. When Gary Seven follows her in a few moments later, the door has nearly closed itself and the lights inside are off. (00:20:25)
Continuity mistake: In the briefing room, Hengist and the Prefect are sitting in chairs against the wall at least a foot apart, with bright overhead lighting that casts no shadows on the wall behind them. When we cut to a two-shot of them, however, they're suddenly shoulder-to-shoulder with almost no space between them, and the lighting changes to cast very dark shadows behind them. (00:28:20)
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: In one scene the Enterprise's phasers were pink instead of blue.
Continuity mistake: When Scotty gets drunk and tosses an empty bottle away, there's a dubbed in sound of glass breaking, but when he collapses, the bottle is unbroken at his feet.
Continuity mistake: During the coup attempt, one Capellan fights with the leader and gets stabbed. Before and after he is stabbed, the man's outfit changes entirely (look at the fur scarf, which goes from purple to orange.) His costume also changes color.
Continuity mistake: Dr. McCoy's medical tunic has an engineering patch on it, instead of the science patch it should have.
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)
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.