Continuity mistake: After the heavy door lands on Korob, his right arm is straight down by his side. The next shot of Korob shows his right arm extended away from his body.
Is There in Truth No Beauty? - S3-E5
Other mistake: In the final scene, Kirk is still in the transporter room, but does not have on a visor when the ambassador transports out. Even if he did, humans can still go mad if wearing one and that's why Spock operates the transporter. Spock has his visor on, but then you see Kirk walk out of the transporter room without a visor and he is not going mad.

Revealing mistake: A straight and level seam connecting the top and bottom halves of the tunnel Spock is crawling through is visible.
Suggested correction: Views of the tunnels made before the creature was wounded by Kirk and Spock appear almost perfectly smooth. It is explained that the creature exudes a powerful acid to dissolve the rock. This tunnel was made after the creature was wounded, so it is logical that the wounded portion of the creature would secrete less acid thus leaving an imperfection as the creature tunnels. This could be a case of incredible attention to detail by the set designer rather than an error revealed.
This correction is too much of a stretch to explain a perfect seam by the wounded Horta. Plus, if the Horta was secreting less corrosive substance, then that area would be less eroded, not more. If attention to detail was paid, then the area would have an outward seam, not an inward one.
Tomorrow is Yesterday - S1-E20
Factual error: Towards the end of the show the Enterprise is leaving Earth orbit and heading towards the sun. We see the Earth diminish and the moon appear looking exactly as it does from Earth. From this angle we should be seeing the "dark side" of the moon, which looks completely different. (00:40:50)

Continuity mistake: When Kirk is facing the Horta he has his phaser in his right hand when seen from the front but when seen from behind he has his communicator in his left hand and no phaser. (00:31:00 - 00:38:00)

Visible crew/equipment: After McCoy examines Charlie and they talk about how Charlie learned to talk by just listening to the ship's tapes, when Charlie stands up the two actors' marks can be seen on the floor - the short one for Charlie and the longer one for McCoy, where they both will stand momentarily. (00:04:56)
Continuity mistake: When "good" Kirk beams up from the planet, the insignia on his shirt is not there. Then it appears when he's walking with Scotty. (00:03:00 - 00:05:25)
Suggested correction: This wasn't a continuous shot though, we just don't know where they get the insignia, it could have been in his pocket. Both Kirk and Sulu are on the planet's surface without their insignia. And when "evil" Kirk beams up, he too doesn't have it on, even though later he does.
What possible reason could there be for the Enterprise Insignia, which is stitched to every uniform, to be in 'Evil' Kirk's pocket? No character has done this in any episode of Star Trek. They don't get them from anywhere, they are a part of their uniforms.
Factual error: In the opening scene on the bridge, when Spock states the planet's properties, the circumference is given in US miles; the mass is given in metric tons; the density is given in metric grams per cubic centimeter; and the atmosphere is given as oxygen/nitrogen. No scientist of Spock’s standing would mix US and metric unit systems. The atmosphere composition should also be stated reversed as “nitrogen/oxygen” with the most abundant gas first. (00:42:00 - 00:59:00)
Suggested correction: That might only true in today's standards. But we have no idea what future generations will choose to make standard.
This is such a trivial criticism that it should be removed to be fair. Whatever measurement standard is used in the future, it will be uniform without mixing of different unit systems.
But that's an assumption based on what you think the future would be like. The British and Americans currently use a mix of different unit systems. While many US students use miles and pounds, they still calculate density as g/cm3.
Deliberate mistake: Special effects of the ship in space were very expensive in the 60s and couldn't be wasted. So when a larger model was built with slightly different nacelles, shots of both versions became common, even within the same episode. This is why the Enterprise sometimes had red needle-tipped nacelles and sometimes lighted "spinning" ones, and in aft views she had either round white spheres or perforated vents at the nacelles' ends.
Plot hole: Pike says he doesn't want women on his bridge, Number One being the one and only exception, and he keeps ordering Colt off it. His apology to Number One indicates that A) he doesn't think of her as female, and B) she's the only exception to his rule. So how does he overlook the very female crew-woman seated at the science station? (00:06:55)

Continuity mistake: When Capt. Kirk and Charlie enter the turbolift heading for the bridge, Kirk is wearing one style of tunic and when the turbolift arrives on the bridge, Kirk is wearing a completely different tunic. (00:15:14)
Shore Leave - S1-E16
Visible crew/equipment: You can see the shadow of a boom mike on a tree just after the Caretaker appears. (00:44:05)
Visible crew/equipment: When the doctor is mixing the drink and Pike gets up off the bed to accept it, an equipment shadow sweeps across the left side of the screen. (00:03:55)
Continuity mistake: All during the episode there are scratches on the left cheek of the "evil" Kirk. When the "Good" Kirk and the evil Kirk confront each other on the bridge, there's a shot where the scratches are on the right cheek of the evil Kirk.
Visible crew/equipment: After Kirk hits Kras with an arrow Spock's arrow hits a Capellan on the cliff, and when the Capellan falls into the bush, a crew member wearing sunglasses and a white T-shirt is visible at the left side of the screen. (00:43:50)
Plot hole: Because of the magnetic ore on the work clothes of the man who beamed up, the transporter made duplicates of everything put through it, and so couldn't be used. This was further complicated by the control and power circuits being blasted by the "evil" Kirk. However, the ship carries a number of shuttle craft, which no-one mentions.
The Man Trap - S1-E2
Revealing mistake: Just after Kirk stuns Crater with his phaser, he gets up to get to Crater, when he does he bumps into a heavy stone monument,a prop that shakes visibly on contact. (00:36:58)
The Gamesters of Triskelion - S2-E16
Visible crew/equipment: When Chekov's drill thrall sits down and nuzzles up to him in his cell, the boom shadow is visible on the wall at the upper left corner of the screen. (00:14:50)
Character mistake: Lt. Joey said to Lt. Sulu "You don't outrank me and you don't have pointed ears" but Joey is a junior grade lieutenant so Sulu would outrank him.
Where No Man Has Gone Before - S1-E4
Continuity mistake: When Kirk is fighting Gary Mitchell, his tombstone reads James R. Kirk. Kirk's middle name is Tiberius. Mitchell is a friend of long standing and would not have got it wrong. (00:44:30)