Audio problem: When Uhura apologizes to Spock for interrupting him playing his instrument, her word is cut off mid speak between cuts. She says "I'm sorr-." But it's close enough it easily got past the editor or the editor cut her word off too soon not realizing. (00:09:59)
Continuity mistake: Just before Uhura begins to hum with Spock's playing of his instrument, she is leaning over a table where they are playing cards. She has one hand on her cheek and then brings the other up to her face as well. When it cuts to a side angle, she's suddenly bringing her hand up to her face again in a repeated action. (00:09:47)
Continuity mistake: After Bones finishes examining Charlie, they move to the door and Charlie begins to put his jacket back on. In the side shot, he gets it on and begins to adjust it around his shoulders when it cuts to a frontal view. Suddenly his arms are relaxed like he's already had the jacket on for a few seconds and in a comfortable position. (00:05:18)
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
Visible crew/equipment: When Kirk and the landing party are standing on the transporter pads ready to beam down to planet, the camera pans to the right as the transporter operator stands at the console, and the end of the set is visible with black cables lying on floor. (00:07:15)
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)
A Taste of Armageddon - S1-E24
Visible crew/equipment: When Mea 3 escorts Kirk and his landing party to Anan 7 and members of the High Council, while the group enters the room the actors' marks are visible on the black rug, as they all stand at their marks. (00:06:55)
Space Seed - S1-E23
Visible crew/equipment: When the landing party are aboard the Botany Bay talking about it being a sleeper ship, Kirk asks if it's possible they're still alive, and as the camera follows Kirk the shadow of the camera/cameraman is visible on the wall, at the right side of the screen. (00:06:25)
The Return of the Archons - S1-E22
Visible crew/equipment: After Scotty tells Kirk that the shields are unable to deflect the heat beams, the piercing soundwaves knock everyone out, and when Kirk awakens in the cell he tries to wake Spock, then the shadow of the camera is visible on the pillar as it follows Kirk. (00:25:55)
Visible crew/equipment: When the Metron returns Kirk to the Enterprise he reappears on the bridge, and the actors' chalk marks are visible on the floor where Kirk and crew stand. (00:47:20)
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)
The Corbomite Maneuver - S1-E11
Visible crew/equipment: After the Fesarius destroys the recorder marker, when Balok declares that Enterprise must also be destroyed, in the next wide shot there's a tape mark on the floor near Bailey, and another one in front of Kirk's feet. (00:21:50)
Where No Man Has Gone Before - S1-E4
Visible crew/equipment: While Kirk is armed with a phaser rifle he quietly moves closer to Gary and Dr. Dehner, but when Gary senses the "foolish man" he causes a boulder to roll past Kirk, and the arm of a crew member is visible behind the boulder pushing it forward. (00:39:40)
Where No Man Has Gone Before - S1-E4
Visible crew/equipment: While Kirk, Spock, and Dr. Dehner are with Gary in sickbay, when Gary makes threatening remarks and gets out of his bed, the shadow of the moving boom mic is visible on the wall at the left side of the screen. (00:28:55)
Revealing mistake: When Kirk holds a golden egg, a seam can be seen on it. (00:43:55)
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.
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.