In the first shot on the bridge, Sulu is seen at the helm but hen disappears to be replaced with a noticeably taller helmsman with similar black hair and darker skin.
Trivia: The ship that Khan stole was of the DY-100 class. The S.S. Botany Bay's number was DY-103.
Despite the fact they say that McGivers is knowledgeable about the late 20th century, she seems to know almost nothing about the Eugenics Wars, and there is no indication of any 20th century paintings, statuary, etc., in her quarters.
When Khan first asks McCoy to speak to the captain, the doctor depresses the button on the com panel, and without him saying a word, the bridge answers. The com isn't a "hotline" to the bridge, so it wouldn't have connected there unless he called for it specifically.
After the Enterprise determines the ship they find doesn't have life signs or charged weapons, they are still at Red Alert for no apparent reason.
The reception for Khan is said by Kirk to be an official dinner, yet only he, Spock, McCoy, and Scotty wear dress uniforms. Everyone else, including Uhura, wears standard uniforms.
As ship's historian, McGivers should have a blue sciences uniform, but wears the red of Engineering and Security.
It is constantly said that Khan had been in stasis two centuries (200 years). But the show takes place in the mid to late 23rd century, so it is actually closer to three centuries.
When Khan states that he will save Kirk if any of the officers join him, it seems that it would make more sense for someone to say "Sure, I'll join you" and then betray Khan later on (as McGivers does), instead of just sitting there watching the Captain die.
Why do they announce over the comm system that Kirk is on his way to Engineering to go after Khan...where Khan is, listening in on the comms? Can't they figure he might hear them say Kirk's heading his way?
Both Scotty and Kirk say they knew about Khan - Scotty says he had a sneaking admiration for Khan, and Kirk says he was the "best of the tyrants." So why the heck don't they recognize him, or at least figure out that the guy in their ship named Khan from the year 1996 might just be related to the guy they're admiring named Khan from 1996? And why aren't there any pictures of Khan in 1996 they could check their passenger against?
When McGivers recompresses Kirk, the "inches of mercury" on the gauge (the measure of vacuum) move to a higher number, which indicates a higher vacuum reading: 30" HG being a perfect vacuum.
When the landing party beams over at the beginning, the transporting officer is wearing a blue jumpsuit, but when they go to the closeup of his hands, they have a red uniform, two braid stripes, and are the standard shot they use when Scotty does the transporting.
As Khan decompresses Kirk, the gauge on the wall says 10 HG and then drops. But in a camera shot a couple of seconds later it says 20 HG.
The Eugenics Wars occurred beginning in 1993 and seem to have been a World War. yet in the Next Generation we find out that World War III doesn't occur until the 21st century. The Eugenics Wars sure seem like they would be considered a World War.
While he's suffocating Kirk recommends that five of his bridge officers receive commendations but there's seven crew on the bridge. Did the other two not suffocate heroically enough for him?
This is the first but not the last time that Kirk turns over the ship's library to a possible dangerous visitor who, sure enough, uses the information to take over the ship.
Lt. McGivers didn't have the gold braid to be a lieutenant, she was an ensign but was always called "lieutenant".
In the scene where they discover Khan in his sleep chamber still alive, Kirk loses his phaser. It falls off of his belt onto the floor as he bends down, Dr. McCoy notices it, and reaches down and shoves it aside as they finish the scene.
In the engine room fight scenes between Kirk and Khan, the use of stunt doubles is very obvious.
McCoy: The Eugenics Wars of the 1990s.
Spock: Your attempt to improve the race by selective breeding.
McCoy: Oh no not our attempt, Mr. Spock. A group of ambitious scientists.
Kirk: Those men went out to tame a continent, Khan. Can you tame a world?
Khan: Have you ever read Milton, Captain?
Kirk: Yes, of course.
Kirk: (to McGivers, referring to Khan) Given the choice between court martial, and accompanying him there, which do you choose?
McGivers: I'll go with him, Sir.
Khan: A superior woman. I will take her.
Scotty: It's a shame for a good Scotsman to admit it, but I'm not up on Milton.
Kirk: The statement made when Lucifer fell into the pit. "It's better to rule in Hell than serve in Heaven."
Khan: I should have realized that suffocating together on the bridge would create heroic camaraderie among you.
Khan: Improve a mechanical device and you may double productivity. But improve man, you gain a thousandfold.
Kirk: If I can have honesty, it's easier to overlook mistakes.
Spock: Insufficient facts always invite danger.
Spock: Superior ability breeds superior ambition.
Khan: Go! Or stay! But do it because it is what you wish to do!
Spock: It would be interesting, Captain, to return to that world in a hundred years and to learn what crop has sprung from the seed you planted today.
Kirk: Yes, Mr. Spock, it would indeed.
Spock: Gentlemen, this romanticism about a ruthless dictator is...
Kirk: Mr. Spock, we humans have a streak of barbarism in us.
McGivers: I don't know if you'll like living in our time.
Khan: Then I'll have to remold it to my liking.
Khan: You are an excellent tactician, Captain. You let your second-in-command attack while you sit and watch for weakness.
Kirk: You have a tendency to express ideas in military terms, Mr. Khan. This is a social occasion.
Khan: It has been said that social occasions are only warfare concealed.
Khan: [to McGivers] My name is Khan. Please sit and entertain me.
Kirk: Very interesting. You ready (to transport), Bones?
McCoy: No. I signed aboard this ship to practice medicine, not to have my atoms scattered across space by this gadget.
Kirk: You're an old-fashioned man, Bones.
McCoy: A pity you wasted your life on command, Jim. You'd have made a fair psychologist.
Kirk: So much for my theory. I'm still waiting to hear yours.
Spock: Even a theory requires some facts, Captain. So far... I have none.
Kirk: And that irritates you, Mr. Spock.
Spock: I am not capable of that emotion.
Kirk: My apologies, Mr. Spock.
Kirk: I thought you said it couldn't possibly be an Earth vessel?
Spock: I fail to understand why it gives you pleasure to see me proven wrong.
Kirk: An emotional Earth weakness of mine.
McCoy: Well, either choke me or cut my throat. Make up your mind.
Khan: English. I thought I dreamed hearing it. Where am I?
McCoy: You're in bed, holding a knife at your doctor's throat.
Khan: Answer my question!
McCoy: It would be most effective if you would cut the carotid artery, just under the left ear.
Khan: I like a brave man.
Although Chekov was not on the show when this episode aired, Khan still recognizes him in Star Trek II. It is a general fan consensus that Chekov was on the ship during "Space Seed," but was not assigned to the bridge yet. Walter Koenig jokes that he believes Chekov accidentally made Khan wait an uncomfortably long period of time to use the bathroom.
The SS Botany Bay DY100 model shown in this episode was reworked and featured in the second season episode "The Ultimate Computer" as the Woden (NCC-325), an old-style automated Federation Antares-type ore freighter and is used as target drone.
Ceti Alpha V, where Kirk exiles Khan, McGivers and the rest of the Eugenics Wars' augments from the S.S. Botany Bay, is featured in the Star Trek: Enterprise episode "Twilight", as the planet where the remnants of humanity gathered after Earth's destruction by the Xindi weapon.
This is the first episode to mention the Eugenics Wars. This final World War, in the mid-1990's, is referred to many times in the Star Trek spinoffs, most recently in Star Trek: Enterprise episodes: "Borderlands (1)", "Cold Station 12 (2)", and "The Augments (3)." Dr. Arik Soong (Brent Spiner) starts out as a believer in eugenic science raising a group of Eugenics War era augments from embryos placed in artifical wombs.
This story is the basis of the 1982 movie sequel Star Trek II: The Wrath of Khan.
Khan: Have you ever read Milton, Captain?
Kirk: Yes. I understand. ...
The statement Lucifer made when he fell into the pit: "It is better to rule in hell than serve in heaven." Actual quote is "Better to reign in Hell, than serve in Heaven." John Milton, Paradise Lost, Book I, line 263
Khan preferred a rough world, such as Ceti Alpha V, to the heaven of Kirk's world.