Continuity mistake: In the training simulator at the beginning of the film, after Sulu and McCoy have both fallen, McCoy has his head resting on Sulu's hip at first. Then, in the next shot, his head is resting closer to Sulu's knee. (00:05:50)
Other mistake: On board the USS Reliant as it orbits Ceti Alpha 6 the systems panels show ship diagnostic diagrams including a wire model of a Constitution class hull, something the Reliant doesn't have. (00:13:01)
Revealing mistake: When Chekov and Terrell are walking on Ceti Alpha V watch as they get to the ridge overlooking the Botany Bay. Each of them cast two very distinct shadows, indicating two separate light sources. The planet only has one sun. (00:15:05)
Plot hole: Khan said that the crew of the Botany Bay had been stranded on Ceti Alpha VI for 15 years. Considering that most of his crew were in their 20s, wouldn't that mean they were all children when they were first stranded? In the original TV series, all of these superhumans were already adults, so how come Khan was the only person to age? (00:19:40)
Plot hole: Why doesn't Reliant know that Khan is exiled here? The Federation is so terrified and opposed to genetic engineering that it's still illegal 300 years after Khan. So why is there no warning along with the data on the Ceti Alpha system? Kirk logged what happened with Khan and his solution of marooning him. Starships use nav data to navigate star systems. Ceti Alpha 6 exploded, yet the helmsman or computer never noticed that there is one less planet than there was when Kirk was there? There is no debris from the explosion? Ceti Alpha 5 is the exact same size and was conveniently blown into the exact same orbit as Ceti Alpha 6 used to have? So there is nothing whatsoever to make the crew even suspect that it's not 6? Enterprise would have to have scanned the planets in the system to know that one was habitable for Khan. Did Ceti Alpha 6's destruction somehow magically turn Ceti Alpha 5 into its exact duplicate? If Starfleet ships have been there to map after Ceti Alpha 6 exploded, none of them bothered to check on the exiles? Pretty callous for Starfleet, don't you think? With the technology and amounts of information available to Starfleet vessels, there is NO logical reason for the Reliant to think that this planet is Ceti Alpha 6. Finally, would the Federation be willing to test a device whose exact effects will be unknown on a planet so close to another inhabited one? (00:21:00)
Suggested correction: The answer is yes: against all known laws of science, the inexplicable explosion of Ceti Alpha VI led to Ceti Alpha V conveniently taking its orbit and making it easy to mistake for its former sister planet. A mistake would've been to give an explanation that can be debunked. By leaving it to "somehow" the movie leaves it open to a million possible rationalizations. You can even make a whole other story about the crazy circumstances that led to this incredible result.
Character mistake: While Khan is "interviewing" Chekhov and Terrell, he stated, "On Earth, two hundred years ago, I was a prince, with power over millions." The official date for this movie is 2285. That would place Khan on earth around 2085 by this statement. However, it is made clear in the episode "Space Seed" that Khan and his followers escaped earth in the year 1996: nearly one hundred years earlier. Quite a way off to be a rounding error. (00:21:45)
Suggested correction: I don't believe the earth year had been established when this movie was made and it was something the franchise applied to itself retroactively later on.
Audio problem: When Kirk says, "Stop energizers," watch his lips closely - he really says, "Stop engines." Mike Okuda points this out in the text commentary on the Director's Edition DVD. The reason the line (and also the one following it) was redubbed was because someone pointed out during post-production that the engines couldn't simply be stopped on a dime. (00:39:08)
Continuity mistake: When Spock is kneeling in his quarters, talking with Kirk, a shot facing Spock's front shows that the bottom of the lighted mirror on the wall is behind his head. In the next side shot, it's not there as he is now much further from the wall and the mirror is out of the shot at right. The angle of the second shot does not excuse the mistake- the mirror should still be visible at the new angle. (Director's Cut DVD). (00:39:30)
Continuity mistake: In the scene when Khan first opens fire on the Enterprise, the exterior shots show the damage on the forward part of the engineering hull. However, the damage on the interior shots is occurring on the aft section. Which is to say if the exterior and interior damage lined up the way they're supposed to, Scotty and his cadet engineers would've all been killed in a warp core breach. (00:50:15)
Continuity mistake: When Engineering is taking damage and the trainees are fleeing, Scotty's nephew goes to the aid of an injured crew member. A containment bulkhead is lowering to seal the compartment as he approaches it and as the shot ends, the bottom of the door has reached the lowest edge of the round collar at the left of the screen. Moments later, the actual rescue is shown while the door is lowering through the same area as before- having started higher than it was when the prior shot ended. The change in camera angle is not creating an optical illusion. (Director's Cut DVD). (00:50:35)
Continuity mistake: When Scotty's nephew dies in Sick Bay, McCoy is holding him up a bit. The wide shot shows Mccoy's thumb is up near the young man's ear, but close-ups of the boy show the thumb isn't there because McCoy's hand is lower on his back. (Director's Cut DVD). (00:58:15)
Continuity mistake: After the Reliant attack, when Scotty's nephew is talking to Kirk in sickbay, he asks Kirk if the word is given, and Kirk takes his bloody hand then places it against his tunic. After he dies, the next scene shows the bloody handprint in a totally different spot on the tunic. (00:58:20)
Continuity mistake: When McCoy bumps into a hanging body's arm and yells 'Jim.', the next shot shows Kirk lowering a body from an upper level by rope. To his right, another body dangles (feet point up, frontside visible). In the following close-ups of Kirk, this body is much closer to him and is turned over (feet point down, backside visible). No time compression occurs between the two shots. (Director's cut DVD). (01:03:55)
Other mistake: When Captain Terrell shoots himself with the phaser, the phaser disintegrates along with his body, when it should have just dropped to the ground (as often shown in the various Trek TV shows). It wouldn't make sense to explain that the phaser disintegrated because Terrell was touching it, because then it would be impossible to explain why nothing happens to the ground that people are standing on when they get shot (Director's Cut). (01:11:20)
Continuity mistake: After being marooned inside Regula I, McCoy is tending to Chekov who is lying unconscious. He says, "He's coming around." You then see McCoy handing him a bandage to hold to his ear and Chekov raises his arm to hold it. Immediately following, there is a shot of McCoy saying "...She's finished," (referring to the Enterprise) and you can see Chekov raising his hand to his ear again. (01:14:05)
Continuity mistake: In the Genesis cave, Kirk puts on his glasses to look at his watch. In the very next shot, he is not wearing his glasses. (01:15:20)
Continuity mistake: When Reliant is hit, a large piece of debris falls to the deck, killing Joachim. In the wide shot as Khan makes his way to the debris, a large mass of hanging wires dangles from the ceiling, lower than Khan's head while he is bent over. But the next closer shot has Khan standing erect, lifting the debris, and the wires have vanished. (DVD Director's Cut). (01:28:20)
Continuity mistake: When Khan's number one officer is dying in the arms of Khan, they exchange a word or two before the first officer dies quite dramatically with his eyes open. Khan then fully embraces the corpse and looks up to the viewer screen and vows to get even with Kirk. However, the "corpse", whose eyes are open, closes them upon Khan's embrace. (01:29:05)
Factual error: Inside the nebula, the Enterprise rises from below and fires a photon torpedo at the Reliant, striking it directly on the dorsal torpedo pod. Watch as the torpedo hits and the pod explodes. Large pieces of the bulkhead explode outward, then begin to fall downward towards the saucer section before they cut camera angles, despite there being nothing dragging them in that direction. (01:31:25)
Continuity mistake: When Spock gives the neck-pinch to McCoy, who slumps to the floor slowly, the floor inside the chamber is a dark-tan/light-brown color, but the close-up of the mind-meld on McCoy's face shows the same floor lit prominently with blue lights. (Director's Cut DVD). (01:35:40)
