The Man Trap - S1-E2
Continuity mistake: When the creature makes it's way through the ship and finds McCoy's room, it stops near the wall with a red vent behind it. It changes back to Nancy in a dissolve cut, but suddenly it's much closer to the walk and is now closer to the vent, something that would not have happened by a simple morph like seen before. (00:28:45)
The Man Trap - S1-E2
Continuity mistake: When Kirk is telling Crater that he needs him and his wife to stay on their ship till he finds out what killed his man, Kirk has his arms crossed. When Crater steps up to him and the angle changes, Kirk's arms are suddenly down at his side. This continuously changes back and forth between shots. (00:18:07)
The Man Trap - S1-E2
Continuity mistake: Kirk jokes with Bones after they land about flowers and is holding some hay or grass in his hands. After Bones makes the comment about bribing girls, Kirk lowers his hand off screen but with the grass still in it. It jump cuts to a different angle from further away and suddenly his hand is empty, and there is no grass on the ground where he could have dropped it. (00:00:57)
The Return of the Archons - S1-E22
Continuity mistake: After Kirk and the landing party beam down, they are met by a man who tells them where they can stay for the night but they will have to hurry because it's almost the "red hour." At that time the camera shows a clock that reads 5:58. After being introduced to the daughter of the man who can give them shelter, a gong rings and magically it is 6:00, 2 minutes later, although only 32 seconds of real time has passed. (00:05:18 - 00:05:50)
Operation -- Annihilate! - S1-E30
Continuity mistake: After Kirk orders Uhura to reestablish contact with Aurelan's transmitter, when Uhura replies that they do not acknowledge her contact signal, Uhura's communications earpiece is not in her ear, but in the next shot it's suddenly back in her ear. (00:06:10)
Continuity mistake: When Kirk informs Galileo that all systems are clear for takeoff, in the shot from inside the shuttlebay as Galileo turns to launch, the shuttlecraft Columbus is also in the hangar deck, but when Galileo exits Enterprise the Columbus is gone in the exterior shot. (00:01:45)
Space Seed - S1-E23
Continuity mistake: As the away team observes Khan in the stasis chamber, McCoy holds his tricorder with both hands, but the next shot shows him holding it in one hand.
Space Seed - S1-E23
Continuity mistake: On the Botany Bay, McCoy is not holding his tricorder, but when the ship's lights activate, McCoy suddenly has his tricorder in his hands.
Space Seed - S1-E23
Continuity mistake: When Khan asks Kirk "How long?" Kirk's head is near Khan's with nobody behind his head, but the next long shot shows Scotty behind Khan.
Space Seed - S1-E23
Continuity mistake: Khan's hands switch positions several times on the table between quick cuts as he and Kirk talk.
Continuity mistake: As Veena (as the Orion Slave Girl) dances, the water in the pool is still, then in the Observation room, as Kirk and party watch, the water is disturbed. A moment later, it's flat calm.
The City on the Edge of Forever - S1-E29
Continuity mistake: When trying to catch McCoy, Kirk's pants get dirtied. After coming out of the Guardian's time portal in the Depression, his pants are clean.
Continuity mistake: In the finale of the fight between Kirk and Finney, Kirk's shirt is torn, exposing his right shoulder and arm. As Kirk (the stunt double) goes for the knock out blow, the shirt is only a little torn in the front. Then the close up on Kirk catching Finney, his shoulder is exposed again.
Continuity mistake: While Kirk questions Spock about his command decision on the Galileo, shots of Uhura and Mears show the ladies close together at Uhura's station with Mears' hands hidden but close up shots of McCoy show Mears and Uhura in the background further apart from each other and Mears' hands in front of her body.
Continuity mistake: As Scotty starts prying the panel open, it's with a tool in his right hand, and the thumb of his left. After the cut, he's suddenly holding it in his right hand.
Continuity mistake: As Christine goes to put the respirator in place, she uses her right hand. After the cut, it's her left that puts it in place.
Continuity mistake: As Bones works on Joe's injury, a red light turns on over his head shining down on the area, illuminating his hair. A second later, the red is gone, then back.
Continuity mistake: The indicators radically change positions when Spock gets on the bio bed.
Continuity mistake: When Sulu confronts the men in the corridor, his epee goes from perfectly straight to having a slight crook, then back to straight when he appears on the bridge.
Continuity mistake: As Joe draws back and stands up, he pulls a knife. First, it's sharp side up, then it's suddenly blade down.
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.