Plot hole: The law officer who arrests Kirk recalls hearing Kirk call the "spirit" Bones. But he wasn't there when Kirk spoke to McCoy. He rushed into the scene several minutes later. If he's lying, how would he know that Kirk used the name Bones? He wasn't there to hear it. Even if he had been, Kirk did not refer to McCoy as Bones in that conversation. (00:10:50 - 00:19:50)
Star Trek (1966)
2 plot holes in All Our Yesterdays - chronological order
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.
Who Mourns for Adonais? - S2-E2
Trivia: An ending that was planned but abandoned for this episode would have revealed that Lieutenant Palamas was pregnant with Apollo's child.
The Corbomite Maneuver - S1-E11
Question: At the beginning, Mr Sulu calls for Captain Kirk to report to the bridge, but Kirk in sick bay does not get that message. Why?
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Answer: Kirk was getting his physical and Dr. McCoy probably turned off communications, because if he hadn't, Kirk would have left and headed straight for the bridge, leaving McCoy irritated.