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!
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.
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.
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)
Continuity mistake: When Sybok is alone with Kirk, McCoy and Spock, revealing their hidden 'pain', his robe is constantly reshaping itself from shot to shot. At one point, when McCoy grabs Sybok, the robe unwraps from Sybok's left shoulder, but is wrapped around him again seconds later. This continues noticeably through the entire scene. (01:06:55)
Continuity mistake: At the camp fire the whiskey bottle never empties. Almost empty, then full again.
Continuity mistake: As the shuttle nears the ship, they stop and are looking at the port side of the Enterprise. Inside the shuttle, as Talbot turns from looking out, the shuttle is pointed directly at the aft section, towards the shuttle bay. The it's back to port to begin the risky maneuver.