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.
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)
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)
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)
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)
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.