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: After the Reliant ambushes the Enterprise, Kirk tricks Khan and hammers the Reliant into retreat. As Kirk turns to assess damage to the Enterprise, Scotty inexplicably appears on the bridge, carrying the charred body of Midshipman Peter Preston. Why on earth would Scotty bring the dying Preston to the bridge, rather than to SickBay with all the other injured? He had to deliberately bypass SickBay just to make an unnecessary appearance on the bridge.
Answer: At the time of the attack, most of Scotty's crew were attempting to flee a coolant leak caused by the damage. Cadet Preston (Scotty's nephew) remained at his post in the confusion, and was the reason the Enterprise was able to maintain minimal power with the energizers knocked out. Although he was wounded from the assault while rescuing another crew member, the coolant leak is what led to his ultimate demise, as the coolant was highly toxic. When Scotty brought him to the Bridge, he was himself quite disorientated from the events and was also devastated by his nephew's condition. Agreed it makes little to no sense, but Scotty didn't know what he was doing. His nephew was going to die, regardless of where he took him to. Going to sickbay would not have prevented it at this point. It seems like it was used as a mood breaker for the scene, crews celebrating their escape from death only to be confronted by it again in another form.
Answer: I believe Preston was already dead at that point. An earlier scene was edited out of the film that explained Preston was Scotty's nephew (his sister's son), and which may account for Scotty's rather odd reaction of first bringing him to the bridge.
Yet Preston is shown alive (still dying) in the SickBay moments later. Preston shares last words with Captain Kirk before he actually dies. So, this is a case of bad editing?
What was edited out of the film was an earlier explanation that Preston was Scotty's nephew-this was way before the Enterprise was attacked.
These scenes, which include several of Preston's lines which were cut, were restored in the 2002 Director's Edition. Curiously, when the film is aired on TV they still run the original video cut which has the scenes removed. The editing is really sloppy with the scenes cut out and the scenes establishing that Preston is Scotty's nephew add another emotional layer to the film. It makes Scotty's actions make so much more sense, he's overcome with grief over his nephew and anger at Khan. With the scenes cut what Scotty does makes very little sense.
In the novelization, I believe it is explained that the ship is badly damaged enough that Scotty reached the bridge while attempting to get to sickbay because the computer glitched.
Question: When the Enterprise recovers Chekov and Captain Terrell, they just accept Chekov's and Terrell's false explanation, even though McCoy is standing right there with a medical tricorder. Why didn't McCoy's medical tricorder pick up the Ceti eels lodged in the brains of Chekov and Captain Terrell?
Answer: Lt. Marla McGivers was the crew member.