Continuity mistake: The blood stain on Kirk's jacket keeps moving around.
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)
Revealing mistake: When the Enterprise is leaving space dock, look at the right (starboard) side of the ship. You can see the shape of the mounting arm the model was mounted on, even though it was blacked out to look like space, and it also blocked out the bottom of the dock. The footage was reused from Star Trek: The Motion Picture.
Trivia: As the shuttle with Kirk and company approaches the Enterprise in Space dock, Sulu says "I'm delighted. Any chance to go aboard the Enterprise..." According to IMSDb.com, there was a full dialog between Kirk and Sulu in the original script. The rest of Sulu's line was "however briefly, is always a chance for nostalgia." Kirk also told Sulu the he had cut the orders for Sulu to Captain the Excelsior.
Trivia: This movie is basically a retelling of another story. When the camera first pans the shelves of the Botany Bay it stops and centers on one book on the shelf in particular.....Moby Dick. That is what this movie is about. Khan is Ahab, The Enterprise is Moby Dick. At one point in the book the whale is circling Ahab's ship on the ocean. At one point in the movie the Enterprise is circling the Reliant (Khan's ship) in the Motara Nebula. Ahab had a scar up one entire side of his body given to him by an encounter with the Whale. At the end of the movie Khan has a burn mark/scar up one side of his body as well. Not to mention that Khan quotes from Moby Dick throughout the movie. The last quote he utters is one that Ahab uttered "From Hell's heart, I stab at thee, for hate's sake I spit my last breath at thee."
Trivia: Early script drafts featured Khan gaining psychic powers with the ability to create illusions in the minds of others. One draft even replaced Khan entirely with an original villain who better suited such fantastical mental powers. By the time Nicholas Meyer wrote the shooting script, Khan was reinstated as the villain and the psychic angle was dropped.
Saavik: You lied!
Spock: I exaggerated.
Question: When Khan speaks to Kirk, he tells him that he wants revenge for the death of his wife. Who was Khan's wife?
Answer: This is a reference to the TV show episode that this movie is a distant sequel to. In that episode, one of Kirk's crew falls in love with Khan and helps him take over the ship. When Khan is exiled to the planet, she chooses to go with him. So it would be that after the catastrophic events of one of the planets in that system exploding and causing all sorts of damage to their new planet, she was killed there and Khan blames Kirk for it.
Question: Presumably, the Genesis Planet was formed out of the dust and gas of the Mutara Nebula. But where did its sun come from?
Chosen answer: According to the novelisation of the film the Genesis project was initially designed to be capable of creating an entire solar system. While the focus of the project eventually narrowed down to altering an individual planet, the sub-routines necessary to create a star were still in place and were activated when the device detonated within the nebula.
Question: This isn't technically a mistake per se, but it involves Spock's funeral. Several Enterprise crewmembers are killed during the battle with Khan, and yet only Spock gets a funeral. Perhaps there was a smaller memorial for the others, and Spock got a full funeral due to his status as captain, but why is Kirk only sending Spock's body to the Genesis planet? I imagine he sent only Spocks's body there since in ST3 there aren't dozens of little regenerated human babies crawling around down there.
Chosen answer: I imagine there was a memorial service for everyone killed. Starfleet's policy on corpses is probably to return them to Starfleet HQ where their families can collect them for whatever services or ceremonies they want unless the crewman had left instructions specifying otherwise. There's no telling why Kirk sent Spock's body to Genesis. Based on Sarek's reactions in ST3 he almost certainly went against Spock's wishes, unless of course, Spock left no recorded instructions and Kirk did what he thought would please Spock based on his being highest ranking officer and Spock's closest friend. It also seems very out of character for Spock to just assume that whoever he transferred his katra to would be able to handle it and carry out his wishes (McCoy certainly couldn't!). Ultimately it seems we have to chalk it up to a plot device to base the sequel on.
According to the novelization, Kirk's intentions were to send Spock's remains into the Genesis sun. Lieutenant Saavik altered the trajectory of the torpedo beforehand, due to Spock's desire to see the Genesis effect for himself. The torpedo casing was expected to incinerate when entering the atmosphere. As pointed out by David Marcus in STIII when the pod was detected on the scanners, the gravitational fields were in flux at the time, and the pod had obviously soft-landed on the surface.
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Answer: Lt. Marla McGivers was the crew member.