Plot hole: When the Medusan Ambassador Kollos and Dr. Jones materialize, the latter is wearing a protective visor and Mr. Spock can see that. Spock then mistakenly addresses Dr. Jones as Ambassador Kollos. Spock's suddenly illogical mistake seems odd: why should the Ambassador need to wear a visor? Shortly after, why do both Jones and Spock wear visors while carrying the Ambassador's still closed gasket to his cabin? (00:01:45)
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.
Amanda: And you, Sarek, would you also say thank you to your son?
Sarek: I don't understand.
Amanda: Well, for saving your life.
Sarek: Spock acted in the only logical manner open to him. One does not thank logic, Amanda.
Amanda: Logic, logic - I'm sick to death of logic! Do you want to know how I feel about your logic?
Spock: Emotional, isn't she?
Sarek: She has always been that way.
Spock: Indeed? Why did you marry her?
Sarek: At the time, it seemed the logical thing to do.
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