Revealing mistake: In the Enterprise lab, as a sped up Spock goes to move away from McCoy and Chapel, McCoy's eyes follow his movements rather than looking at where Spock was supposed to be after he "disappeared."
Revealing mistake: As Kirk and company exit through the tunnel, the seams of the wall sections are visible.
Revealing mistake: As Trelane takes a swipe at Kirk, he hits a tree branch. As it breaks away, the building material it was made from is revealed, rather than it being wood.
Revealing mistake: In Trelane's castle, Kirk and Sulu are supposed to be frozen, but they slightly waver.
The Man Trap - S1-E2
Revealing mistake: On the planet, as Kirk and Spock try to get to Professor Crater, Crater fires at and destroys the center support of the arch. As it settles, the parts are clearly hollow. (00:34:21)
Revealing mistake: Chekov covers Mara's mouth with his hand when he assaults her in the corridor. Kirk intervenes and throws Chekov against the opposite wall. Brown streaks form where Chekov's hands hit the wall, most likely from the brown makeup used to create Mara's skin tone. (00:32:20)
Revealing mistake: When Kirk and Garrovick are fighting at the end, Kirk knocks him down. As he helps him up, Garrovick leans against a huge boulder and the papier-mache rock moves very noticeably.
Space Seed - S1-E23
Revealing mistake: Just before Kirk and Khan fight in Engineering, Khan bends Kirk's phaser pistol in half, but the small hand phaser on top is still functional.
Revealing mistake: Just before Kirk finds himself in Trelane's "courtroom", look behind Kirk on the bridge above Spock's work station. The viewscreen with the planet on it is actually a piece of paper that's coming away from the wall.
Shore Leave - S1-E16
Revealing mistake: During the scene with Sulu and the samurai, each actor casts three shadows. Plus as the samurai rushes Sulu, the "sky" appears black behind him.
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.