Revealing mistake: A re-used sickbay scene taken from an earlier episode causes Nurse Chapel to instantly revert to her old hairdo as the sound waves make her fall unconscious. (00:41:00)
Visible crew/equipment: A camera shadow briefly intrudes on the right side of the screen as Kirk asks Mr. Scott about the sensor readings. (00:00:55)
Audio problem: When Kirk demands to know who the Troglytes are, his voice is dubbed over: his lips don't move at all. (00:04:05)
Continuity mistake: During Spock's Court Martial, Chekov says that General Order 4 is the only exception to Starfleet's no-death-penalty policy, and Sulu and the others agree. However, according to "The Menagerie," that exception is General Order 7, not 4.
For the World is Hollow and I Have Touched the Sky - S3-E8
Continuity mistake: After he falls unconscious onto the blue rug, McCoy's position relative to the rug's top edge keeps changing between shots. (00:36:40)
Continuity mistake: When Kara renders the landing party unconscious, Kirk falls with his arms splayed out to each side. But in close-ups, he has one hand folded over his chest. (00:23:30)
Is There in Truth No Beauty? - S3-E5
Continuity mistake: Kirk aims his phaser at a berserk Spock's head and fires, but the beam hits him in the stomach.
Audio problem: Just as Garth brings Spock back and releases Kirk from the cell, "inviting" them to dinner, there's an odd buzzing/rattling noise in the audio that shouldn't be there. (00:11:30)
Factual error: When Kirk is given the medicine badge, it's a stretchy elastic/Spandex headband. This is supposedly a completely pre-industrial culture paralleling the early Native American tribes. They have no fabric, no yarn, no spinning wheels - only hides and animal hair, neither of which can stretch a la Spandex. (00:14:40)
Continuity mistake: The shards of the goblet Spock breaks change quantity and position on the table with the fruit bowl on it. (00:28:30 - 00:31:30)
Revealing mistake: McCoy's stunt double's face is visible several times during the fight with the berserk orderly in the sickbay lab. (00:19:15)
Revealing mistake: After Kirk and the crew arrive underground, he stuns Kira and removes her bracelet. After he removes it, the unconcious woman quite deliberately lays her hand flat on the ground. (00:21:15)
Character mistake: Spock tells Zarabeth he came from a world "millions of light-years away." The galaxy is only about 100,000 light-years across - the area the Federation has explored even smaller.
For the World is Hollow and I Have Touched the Sky - S3-E8
Continuity mistake: Kirk calls Scott to beam up, and lowers the communicator from his face as he looks at McCoy. In the next shot, he's holding it to his mouth once more. The shot changes one more time, and it's lowered again. (00:31:55)
Revealing mistake: Zarabeth tells Spock that Zor Khan only left her what was necessary to survive in the ice age. Mascara, eyeliner, lipstick and hairspray were apparently considered survival necessities. Yes, we know the actress "had" to wear make-up. But in a prehistoric setting, it shouldn't look as though she did. She could and should have been given a more "natural" make-up job - and an unlacquered hairdo. (00:38:25)
Continuity mistake: During McCoy's struggle with the orderly, only half of the plastic colored bottles strewn on the table are knocked off onto the floor. But when Nurse Chapel hurries over to tranquilize the orderly, the rest of the bottles vanish, leaving the table completely clear. (00:19:10)
Continuity mistake: When Garth forces Kirk to kneel at his feet, Kirk's hands are extended palms down, then palms up, then palms down again as the camera angles change. (00:34:20)
Other mistake: At the end, Kirk teases Spock twice specifically about letting himself be hit on the head in order to determine which Kirk was genuine. But the phony Kirk never hit Spock on the head. He merely pushed Spock over and attacked the real Kirk. Clearly, the action sequence wound up differing from the scripted dialogue, and no one noticed. (Also clearly, Kirk is not speaking metaphorically here.) (00:45:30 - 00:49:20)
The Empath - S3-E12
Continuity mistake: In the opening scene inside the underground station, the bright blue mat under the viewer desk chair disappears. (00:00:55 - 00:02:30)
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.