A Taste of Armageddon - S1-E24
Continuity mistake: The landing party had been apprehended and placed in a locked room under the supervision of a single guard. Spock manages to free them and Kirk knocks out this guard, leaving him in the locked room. Later on in the episode, they return to this very room and somehow this guard is gone. He could not have woken up and walked out because it is a locked room and Kirk took his key. (00:23:45)
Tomorrow is Yesterday - S1-E20
Other mistake: The Air Force police officer (played by Hal Lynch) was beamed up from inside the records room (after finding Kirk exiting the dark-room) but was returned outside the room... so he was physically transported INTO himself (as opposed to replacing the beamed-up future version at the exact moment and place he was removed as they did the pilot, Christopher).
The City on the Edge of Forever - S1-E29
Factual error: When Edith Keeler is killed by the truck, it is traveling at about 25 miles per hour. At that speed and her weight around 120 pounds, she would have been thrown about 50 feet. However, she's seen dead on the ground in front of the mission where she was hit.
The Conscience of the King - S1-E14
Plot hole: After Kirk sees Leighton laying next to the rocks, he rushes over to examine him. He places one hand on Leighton's arm and the other on Leighton's waist and declares "It's Tom Leighton...he's dead." All this without the use of a medical tricorder or even the experienced opinion of the ship's doctor to confirm what Kirk is seeing. (00:10:46)
Other mistake: Stiles gives a countdown for impact to Kirk saying "estimate it will overtake us in two minutes, sir." After only 31 seconds, Sulu starts his own countdown, saying "5, 4, 3, 2, 1, impact." Only 55 seconds have passed from the time Stiles started his countdown to actual impact. Everything was shot in real time without scene changes. Being off the impact estimate time by over a minute doesn't sit well considering a Starship's advanced sensors. (00:29:27)
Continuity mistake: Kirk turns his head and displays a stunned look... a full second before the Gorn even starts to disappear. (00:45:47)
The Man Trap - S1-E2
Other mistake: Sulu is asking Janice why people call inanimate objects "she"? Then gives an example. He says "Like, she's a fast ship." But the subtitles get this wrong and have him saying "Like, she's a bad ship". (00:23:30)
The Return of the Archons - S1-E22
Other mistake: After Sulu is "absorbed", he is beamed up to the ship. After materializing, his demeanor could be described as calm, gentle, meek and euphoric. After that scene, the captain's log quotes Kirk as saying "Mr. Sulu has returned, but in a highly agitated mental state." Was Kirk looking at a different Sulu than we were? A gentle, meek and euphoric condition incorrectly being touted as "highly agitated"? Time for Shore Leave. (00:01:28 - 00:03:53)
Other mistake: While on Starbase 11, Kirk and McCoy watch Pike on a starbase desktop monitor as his light keeps blinking no. When Kirk is with Mendez in his office discussing the Talos IV top secret file, Piper watches Pike on the desktop monitor in the office. Then Spock uses the monitor in his quarters to watch Kirk. All these monitors have the same dings and markings around their screens, which are also the same as other desktop monitors on Enterprise in the previous episode, The Corbomite Maneuver. (00:11:10)
The Corbomite Maneuver - S1-E11
Other mistake: When Kirk is in sickbay with McCoy he uses sickbay's desktop monitor to contact Spock on the bridge, then when Kirk is in his quarters he uses his own desktop monitor to contact Spock again. Both have the same paint dings and smudges around the console screens, revealing the same one was used during filming. (00:04:30 - 00:06:30)
Other mistake: When Kirk is lecturing Ayelborne in the council chamber, the actor behind him is mouthing Kirk's dialogue.
Other mistake: It's been established the planet is extremely dangerous to human life but when Jaeger, McCoy and DeSalle beam down they just have a simple mouth/nose mask on.
Continuity mistake: In the opening, the crewman gets a few drops of the infectant on his hand, but the reddish mass on the wall remains. On the ship, when the spectral view is shown, the red mass is nowhere to be seen.
Deliberate mistake: At the very end, the Talosians send a final visual transmission of Vina and Christopher Pike, now whole and happy and reunited after 13 years, holding hands as they enter the Talosian elevator in the hillside. However, in this last shot, the elevator is still half-disintegrated, exactly as it was 13 years earlier when the Enterprise crew destroyed the hillside with a laser cannon. Within the context of "The Menagerie" storyline, this suggests that the Talosians never attempted to repair the elevator for 13 years (even though they continued using it). This incongruity is due to Gene Roddenberry cannibalizing his Star Trek pilot "The Cage," which contained zero footage of Jeffrey Hunter and Susan Oliver entering the intact elevator together (only the destroyed elevator). So, Roddenberry deliberately tried to "slip one by" the audience in this brief shot.
Suggested correction: There are reasons why the elevator would appear damaged. As the Talosians were in control of everything shown on the ship's viewer, the entire scene could be an illusion, or at least the elevator's condition may have been, with the Talosians choosing to allow the viewers to see the elevator in the same condition they last saw it. Just as likely, however, is that the Talosians truly never did reconstruct the elevator, as the whole point of their having a menagerie of other beings was an attempt to breed a race that could physically serve them, for their concentration on their mental powers had led to a complete inability and unwillingness to perform physical tasks (like repairing an elevator).
Still, as long as the Talosians are creating the illusion of Christopher Pike and Vina in their "restored" bodies, why not create an illusion of the elevator and hillside restored, as well? One big illusion of restoration, rather than a composite of dismal reality and happy-ending illusion? Again, to the point of my original post, the obvious incongruity is due to Roddenberry using the only happy-ending footage he possessed, that of Pike and Vina entering the half-obliterated elevator as they did at the end of "The Cage." Certainly, if Roddenberry only had the foresight to shoot Jeffrey Hunter and Susan Oliver entering the intact elevator, he would have used that footage instead. Any attempt to explain away the 13-year incongruity is mere wishful thinking.
This would qualify as a question, not a mistake. It is entirely plausible that the Talosians wouldn't bother to repair the elevator. It's also possible, as the previous correction points out, that the entire scene is an illusion. Remember, Captain Kirk sees Vina and Pike together on the planet literally moments after Spock wheels Pike out of the room. It's unlikely Pike had already been beamed down.
Revealing mistake: When the Talosians place Christopher Pike and Vina into the "picnic" illusion (in the countryside on Earth), Pike wanders around marveling at how real it all seems. Well, "real" except for the fact that Pike's body is casting 4 distinct shadows in 4 different directions on the ground, the result of studio set lighting.
Continuity mistake: When Sulu first emerges on the Bridge, Kirk confronts him, and standing a couple feet from the rapier. A second later, Kirk's a few inches from it.
Other mistake: In the Transporter room, as the Decontamination field is used, the shuttered lighting casts not only on Spock and Joe, but on the walls surrounding the chamber.
The Return of the Archons - S1-E22
Revealing mistake: The rocks pelting Kirk and the landing party when all hell breaks loose bounce when hitting the actors, the brick walls, and the concrete sidewalk.
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.