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.
Revealing mistake: As Kirk and the Gorn battle, they briefly confront each other from opposite sides of a dead tree which has truncated limbs. One of the larger tree limbs on this supposedly uninhabited, tiny world has obviously been cut off with a chain saw or similar cutting instrument.
Revealing mistake: The stuntman playing Latimer is obvious when he falls after being hit in his back with the creature's spear.
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.
Visible crew/equipment: As the camera swings around to simulate the crewman's gaze, the top of the background is visible for a second until the camera pans down.
Visible crew/equipment: As Kirk goes to talk to Uhura, the studio light is reflected of the second to left panel from Uhura.
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.
Character mistake: When Kor describes the effects of the mind-sifter to Kirk (who is still in disguise as an Organian), he says the machine would leave him "more vegetable than human." There is no reason a Klingon would reference humans while speaking to a person he believed to be Organian.
The City on the Edge of Forever - S1-E29
Factual error: Spock picks a lock during the great depression, but the lock is from the late 50's.
The Return of the Archons - S1-E22
Audio problem: In the transporter room, as Kirk is talking to Sulu, the door opens, McCoy comes in, and the door shuts. Trouble is that the characteristic sound of the door is missing.
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.
Revealing mistake: As Charlie watches the pole lowering into a square hole in the deck, the wood grain of the set piece is visible. The wood has been painted gray/silver to look like metal. (00:06:06)
This Side of Paradise - S1-E25
Plot hole: When Captain Kirk is the last person unaffected by the spores, he's on the bridge lamenting the fact that he is trapped in orbit above the planet since he can't pilot the ship alone. He also can't call for help because Lt. Uhura sabotaged long range communications. but Captain Kirk has somehow forgotten about the shuttle craft. He could have easily escaped on one of those.
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.
Other mistake: After Scotty makes his remarks to Spock, he raises his phaser. The sparks start up before Scotty levels his phaser.
Revealing mistake: As Spock gets to to the helm position, the whole console visibly wobbles as he hits the controls.
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.
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.