Continuity: When Spock and Kirk pursue the Horta, they come to a fork in the tunnel. Kirk points right and tells Spock to go left. Then he points left and says he'll go right.

Continuity: After his initial mind meld with the horta, Spock tells Kirk, "That's all I got, Captain: waves and waves of searing pain." A minute later, he says that it's "a highly intelligent, extremely sophisticated animal" that calls itself a horta. Apparently, waves of searing pain were not all that he got after all. Unlike Spock to be so imprecise.

Deliberate "mistake": Here, as in nearly every other ST episode featuring caves, caverns or mines, all the floors are perfectly flat and the lighting adequate-to-see-by or even brilliant. These configurations are easily found on soundstage sets - but not in nature.

Plot hole: Spock has absolutely no way to know, yet, that the horta only secretes her corrosive substance when tunneling: he hasn't had time to examine her or to do more than determine that she does indeed secrete a substance that cuts the tunnels. So he should at the very least scan the piece of her that falls off before he picks it up with his bare hands. Major lapse of logic, which given his character goes beyond a character mistake.

Revealing: The Horta's round tunnels have perfectly even striations and are obviously factory-manufactured tubes. Acid secreted by an elliptical creature burning through solid rock would not create a perfect circle. The Horta is visibly not chewing, sculpting or smoothing the sides. No acid burning method would leave patterned stripes on the walls, either.

Revealing: Shatner fluffs his line when asking the mining engineers whether they've posted sentries. He asks if they've posted "centuries" instead.