Continuity mistake: After the bird of prey first fires on Enterprise, Kirk is thrown right out of his chair to his left and lands on the floor. The camera pans around the bridge briefly, seeing the rest of the crew staggering and holding onto things. In the very next shot Kirk is back in his chair shouting "back off, back off" and the crew back in their positions as if nothing has happened.
Continuity mistake: When Captain Kirk and the shape shifter are fighting on the planet (the shape shifter looks exactly like Kirk). They are rolling through the snow about to roll over Bones. In one shot, it looks like they will roll over his feet first, and then the rest of his body. In the next shot, it is a little closer and they roll over Bones' right arm first and not his feet first.
Continuity mistake: At the beginning, the USS Excelsior detects an approaching shockwave. One of the bridge officers is standing next to Sulu, delivering a report. When the camera angle changes, the same officer is seated at a console behind two standing crewmen. When the camera cuts again, he's between Sulu and that console, then sits to operate it.
Continuity mistake: In the scene where Lt. Valeris vaporizes a pot of mashed potatoes two things happen. Firstly, only the pot is disintegrated, not the contents (odd) and secondly, a female crew member can be seen walking into Valeris' field of fire carrying a tray. Upon spying the phaser, she wheels about in a 180 degree turn to get out of the way. The camera angle is reversed and she repeats her action of turning around to scoot out of the way after the pot has been destroyed so there is no reason for her to do so.
Continuity mistake: When Kirk is being tried for the assassination of the Klingon Chancellor, his personal log is used against him. Chang was able to get a hold of that clip because Valeris heard him say it while he was making his personal log in his quarters just after leaving space dock. However, in the trial the sound byte says "I've never trusted Klingons, and I never will. I've never been able to forgive them for the death of my boy." When Kirk was recording his log, his exact words were "I've never trusted Klingons, and I never will. I can never forgive them for the death of my boy." Oddly enough, the version used in the trial is less condemning as it simply states that he hasn't yet forgiven them, while the version said in his quarters states that forgiveness is impossible. (00:14:00 - 00:48:50)
Continuity mistake: In the fight against the stealth attacking bird of prey near the end the Enterprise gets a torpedo shot through the saucer section leaving a big hole (it's a clear shot through as you can see it blasting from one side to the other) but later when you see the Enterprise and Excelsior attacking the bird of prey the hole is gone and instead you only see burn marks. At the end of the movie the hole is there again
Continuity mistake: When Kirk and McCoy are arrested on Kronos One, McCoy offers his right hand to the Klingon putting the handcuffs on him, and Kirk's hands are also being cuffed in that shot. Then in Kirk's next shot, 10 seconds later, his hands are being put into the cuffs again. (00:36:05)
Continuity mistake: After the trial, Colonel West and others discuss plans on how to rescue them. The president rejects the plans, which are then left by the group in the president's office. Then a little later the president talks with Gorkon's daughter via view screen and the plans are still there in full view in the background.
Continuity mistake: In the original UK VHS version of the movie, Scotty beams the Klingons aboard the Enterprise using the controls in the booth (located behind a glass screen). The shot cuts from the booth interior to the Enterprise senior officers awaiting the arrival of the Klingons on the transporter pad - Scotty is suddenly in front of the glass and in the line-up. The shot cuts back to the interior of the booth and Scotty is back in there, operating the controls.
Continuity mistake: When Kirk and Sulu are talking about the details of the peace conference, you can see Sulu on the small display behind Kirk. When Kirk asks when the conference starts, you can see on the small display that someone leans in to tell Sulu the information. When the camera cuts to Sulu the person is no longer leaning in but is standing behind Sulu. (01:28:20)
Continuity mistake: It's slight, but noticeable. The nails used to keep Chang's eye patch in place change slightly over the course of the film. For example, when they're beamed aboard the Enterprise, the nail closest to Chang's eye is at the top of the patch. But, during the climactic battle, it's down, closer to his nose.
Continuity mistake: In the opening scene when Sulu is on the bridge and the energy wave begins vibrating the Excelsior, when Sulu's tea cup begins vibrating across the table, it's first seen closer to Sulu. The next close shot shows it vibrating right to the edge of the table. Yet in the next wide shot, it's back where it was near Sulu again. Then in the following close, it's back at the edge, this time sliding off to the floor. (00:04:00)
Continuity mistake: When the Excelsior enters the battle in orbit of Khitomer, General Chang's Bird Of Prey is on top of her. However, when he orders to fire upon her, she is hit from below.