Continuity: The blood stain on Kirk's jacket keeps moving around.

Continuity: 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.

Continuity: While Kahn 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 Kahn on earth around 2085 by this statement. However, it is made clear in the episode "Space Seed" that Kahn and his followers escaped earth in the year 1996: nearly one hundred years earlier. Quite a way off to be a rounding error.

Continuity: When Spock is dying within the glass confines of the ships nuclear power source room with Admiral Kirk (William Shatner) on the opposite side of the glass, in one scene speaking to Spock, Admiral Kirk's red Federation uniform jacket lapel is unbuttoned at the top. In the very next scene the uniform jacket is buttoned.

Other: During many of the scenes of the Reliant in space, you can see stars through the dark parts of the engine nacelles.

Continuity: 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).

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.

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 it's 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?

Continuity: Spock's funeral takes place in Torpedo Bay 1, on the starboard side of the ship. The interior shots, however, show Torpedo Bay 2 (you can see the label and the airlock from the beginning of the movie). Making matters worse, Torpedo Bay 2 was destroyed in the battle with USS Reliant.

Revealing: 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.

Factual error: Inside the nebula, the Enterprise rises from below and fires a photon torpedo at the Reliant, striking it directly on the ventral 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 no gravity in space.

Continuity: 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).

Continuity: 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).

Continuity: 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).

Continuity: 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).

Continuity: 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.

Continuity: 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.

Continuity: The Enterprise is (slowly) attempting to put distance between herself and Reliant (which is about to explode). Whenever Enterprise is shown coming toward camera (or watching Reliant on its viewscreen), Reliant is alternately seen from its starboard side pointing at our 2 o'clock position, from port/aft listing hard to starboard, from it's aft/top area, pointing toward 1 o'clock, and from starboard/bow pointing to 5 o'clock... yet Reliant isn't wobbling or moving, and Enterprise maintains a straight (shortest) course away from her... all suggesting Enterprise is traveling in four directions at the same time. (Director's cut DVD).

Continuity: 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.

Plot hole: Why does the Genesis device have a manually activated timer? The proposal to the Federation clearly shows it was meant to be launched from a ship. We see that it created both a planet and a sun, meaning it's effects must reach the minimum distance necessary between a sun and habitable planet. Further, we see it's effects barely being outrun by warp speed. So the Genesis effect visibly has the destructive range to make a manual timer absurd. Thus, there is no way that the smartest scientists in the Federation would design a device that powerful with that much potential range and give themselves 4 minutes to get clear. Even if they had, no Starfleet captain would risk his ship and crew delivering it that way. The only reason it is there is to give Enterprise a dramatic time window to escape in. And we know that super-intellect villain Khan did not add that feature, since David knew exactly how much time was on the clock. [This is becoming one of those few entries that is being locked purely because there's clearly no obvious resolution to it - people keep arguing back and forth, and it'll never settle. As such it's remaining a mistake - if enough people are really convinced it's not one, then vote it down into obscurity.]