Revealing mistake: 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 mistake: When the "pleasant" Kirk and Spock go down to the engineering level to get the "animal" Kirk, they split up and "pleasant" Kirk meets the "animal" face to face. As he steps out from behind a screen type wall, you can see that the "animal" Kirk is really Shatner's stunt double helping to fill the double role. This can also be told by the size difference when the two are close together and the shot is from behind the double.
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Revealing mistake: When McCoy is examining Charlie in sickbay, several shots of the diagnostic panel show a clear reflection of Charlie's upright profile. But Charlie isn't sitting up during the exam - he's lying flat on the table. The close-ups of the panel were shot while actor Robert Walker Jr. was either sitting or standing nearby.
Revealing mistake: After the ship enters the galactic barrier, when Kirk orders "navigation on automatic" there are flashes of light, and in a closeup of the first console just to the left of the main viewscreen, we can see the special effects material spread across the panel below the controls, for the fire to burn when it explodes. Then it cuts to the wideshot as a second console (near Spock's station) blows up, but in the background that first console is intact - no fire/damage whatsoever (it explodes again in a following wideshot).
Revealing mistake: As Kirk turns to run on the castle steps, an iron bar barricade appears, blocking his path. When it does, watch the castle wall, and the barricade. It seems to slide just a few inches to line up correctly in the shot, showing poor editing.
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