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.
Star Trek (1966)
1 plot hole in The Enemy Within - chronological order
Tomorrow is Yesterday - S1-E20
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)
Trivia: Gene Roddenberry created the transporter as an easier (and cheaper) way of getting Enterprise crew members onto a planet's surface, rather than landing the ship on the planet.
Question: When Kirk and crew neutralized all the androids on the planet, what happened to the androids on the Enterprise running the ship?
Answer: If all the humans beamed down and only Androids were on the ship as Larry Mudd said then how did they get back aboard the Enterprise if all the robots were shut down.
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Answer: After causing Norman to overload, all of the other androids shut down. The same could be said for the androids on the Enterprise.