The Alternative Factor - S1-E28
Plot hole: Kirk knows that Lazarus is insane and that he wants the Enterprise dilithium crystals. Yet he's not restrained in sickbay and is, in fact, given free run of the ship so that he can knock out the crew in engineering and steal the crystals. Other than to further a woefully weak plotline, this makes no sense whatsoever.
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)
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?
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.