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.
Character mistake: Spock expresses amazement that the natives of this planet speak Earth English, however, he and Kirk were both on the bridge when Uhura tapped into the planet's news broadcast and already know that they speak Earth English, and there's no reason to tell McCoy, because he heard it too. Commenting on it would be illogical. (00:07:00)
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.
The Ultimate Computer - S2-E24
Continuity mistake: The doctor and Spock are facing each other, the camera angle changes and they are suddenly shoulder to shoulder. (00:26:50)
The Alternative Factor - S1-E28
Continuity mistake: Lazarus had knocked out the transporter technician, but when Kirk arrives he is fine and operating the transporter. (00:37:35)
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.
Plot hole: How did the android Norman get aboard the enterprise? If he beamed aboard I'm sure someone would have noticed and where did he beam from? The Enterprise was nowhere near any planet and I'm sure they would have detected any spacecraft nearby.
Suggested correction: These are unanswered questions, not plot holes.
But something phrased as a question because it has no decent answer can constitute a plot hole.
The Man Trap - S1-E2
Plot hole: The salt creature needs salt, but there is no need for the creature to kill anybody, just have them deliver a large shipment of salt the next time some ship come to visit the planet.
Suggested correction: As shown several times, the creature is acting on craving and impulse. It's able to not attack Dr. Crater because they have a mutual relationship, as well as he provides salt for her from their supplies. But their supplies are running low, as he even stated they did have 25 pounds of salt but displays a jar with barely any left in it. It is reasonable to assume that he has had to start rationing the supply of salt to her to keep her till they could get another shipment. They were not getting the salt right off after Kirk arrived, and so the creature could not resist the urge to suck salt it needed out of the crewman when they were together alone, reason and logic being clouded by its desire and feral cravings.
Shore Leave - S1-E16
Character mistake: Yeoman Barrows is a crew member on an star ship and I assume has experienced or has trained to experience many different things she will encounter on the tour of duty but she freaks out and cries uncontrollably just because she sees Don Juan.
Plot hole: 300 years is just too long for the children to be on their own. How did they keep their clothes relatively clean for 300 years? Since the kids are playing all day they aren't out in the fields planting and harvesting crops for food, how did they eat?
Suggested correction: For the clothes, it's highly unlikely that they wore the same sets for 300 years. They are in a town/city and on a world that is mostly empty of most human life now. They can easily just find more clothing their size from other houses and even stores. As far as food, children are very good scavengers.
The issue of clothing is not so much an issue as is the issue of food. Given that the children are growing at an incredibly slow rate, their metabolism is probably much, much, much slower and would require far less sustenance.
Continuity mistake: When Spock races back into the phaser control room, he places his electronic tablet on the console and kneels to check on the unconscious Styles and Tomlinson. From one shot to the next, the tablet changes its position on the console behind him. (00:40:00)
Character mistake: Spock tells Kirk that without being able to test their vaccine with the ship's computers, "it could be a beaker of death." The vessel that the vaccine is contained in is a flask, not a beaker. The ship's science officer should know the difference. (00:37:25)
Continuity mistake: After their life threatening surgery, Spock and Sarek somehow manage to switch beds between being in surgery and recovering. (00:45:00)
Character mistake: Kirk is surprised by Spock's behavior, but shouldn't everything about Spock be in his records? Kirk should therefore know about Spock's needs and have planned for them.
The Man Trap - S1-E2
Other mistake: When Crater is hit by the phaser, his collapse is sped up. (00:36:50)
This Side of Paradise - S1-E25
Continuity mistake: As Spock beams up from the planet, Kirk, who is manning the transporter controls suddenly pulls a steel pipe from nowhere. (00:33:55)