Continuity mistake: When Spock, wearing rocket boots, is in the turboshaft carrying Kirk and McCoy on either arm, he fires the booster rockets, thus propelling the three of them up the turboshaft. If you watch carefully, the deck numbers in the background as they rise upwards go as follows: 35, 52, 64, back to 52, 77, 78, and then 78 again! Not content with one goof, Kirk and McCoy can quite clearly be seen with their feet dangling in mid air, not on Spock's boots. They aren't exactly clinging to him either, more like leaning against him. Surely Kirk and McCoy would be unable to hold onto him!
Revealing mistake: When Sybok lifts Kirk off the ground in the shuttle bay, wires are visible holding up Kirk by his legs.
Visible crew/equipment: In the elevator shaft/rocket boot sequence, the 'arm' of the lift device that is actually holding Spock casts a strong shadow on the wall to our right of Spock, indicating the arm goes from Spock's back to the black vertical slot in the right wall. It is most visible as Spock first lowers into view next to Kirk. (01:02:40)
Continuity mistake: When the malevolent entity creates a false image of Sybok, it first has a ponytail, then when the two Syboks grapple, the ponytail is gone.
Revealing mistake: In the beginning of the movie where Kirk falls off the mountain, it's very obvious that he's falling against a backdrop.
Continuity mistake: When Kirk is climbing the mountain, Bones is watching him from a rather great distance away but it takes him only seconds to reach the place where Kirk would have hit the ground after falling down.
Other mistake: If Sha ka ri is in the center of the galaxy then it should have taken about 70 years to reach if the Delta Quadrant is opposite the Alpha Quadrant. Even if this is not so, it has been stated that the nearest point in the Delta Quadrant is 70 years away from earth, therefore the center of the galaxy should not be within travelling distance of earth, or anywhere within the federation.
Character mistake: Near the end of the film, Kirk mentions that he had a brother once, to which Spock appears surprised. Kirk then responds that he was lucky to get him back, referring to Spock's death and rebirth in the second and third films. One problem - Kirk DID have a brother, who died at the end of the original series' first season. Spock doesn't seem like the kind of person to forget about such things, especially as he was nearly killed by the same parasites. Spock's memory may still have been incomplete, although you'd think he'd know such a major detail about his best friend. However, McCoy should definitely remember Kirk's brother, especially seeing as he was the one who pronounced him dead.
Continuity mistake: When Kirk gets a shock from inside a ceiling panel in the brig, he falls off Spock's shoulders. The overhead camera, looking down shows Spock holding Kirk's feet. But when the shot changes to a frontal of Spock, he is holding Kirk's hands (indicating that Kirk actually just jumped up from the floor, with Spock lifting for a bit of extra height, before the shot begins) and we see Kirk landing and rolling. (00:57:00)
Continuity mistake: When Scotty hits his head and collapses in a passageway, he's knocked out and lies prone on the floor with his head closer to the camera than the base of the round archway he is lying near is. When Sulu checks on him, his head is now through the archway- a change in his position of about a foot. (01:01:20 - 01:01:55)
Continuity mistake: When Sybok and the others finally meet 'God', Spock sits against a rock after being struck down. His right arm is down, hand on the ground in a wide shot as 'God' says "a vision you created". Kirk is shown with his right hand on the ground, resting on his right rump. The shot goes to a close-up of Spock, and his right arm is suddenly across his raised knee with no time to have moved there. Then the shot is on Kirk, who is suddenly on his left rump and hand with less than one second to have made the change. (01:30:20)
Continuity mistake: When Sybok makes his speech to the entire Enterprise crew, he begins with his robe conspicuously open, the lapels unrolled and ragged-edged, and it hangs low on his back, while his hands are at his belt. The scene cuts away for a moment, then back to a close up that shows the robe is gathered very high on him- square shouldered, and the lapel area neatly rolled. (00:57:50)
Continuity mistake: When Kirk is talking with 'Bob' on the main viewscreen, various parts and gear are scattered in front of the screen on the floor, including a tall black cylinder that is tall enough to block our view of a portion of the screen's lower white frame area. After a quick close-up on Kirk, the shot is tighter on the viewscreen, but we see the black cylinder is gone, yet from this lower angle, it should be more prominently in view, blocking more of the white frame. Further, in the wide shot, the blue tracer lights beneath the screen are off, but in the tight shot, they are on. (00:29:50)