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.
Other mistake: When Sulu tells Kirk he is coming to help, he states the Excelsior is currently in the Alpha Quadrant. The problem is the the Alpha Quadrant in the Star Trek universe is one quarter of the total Milky Way Galaxy. While technically correct, Sulu giving his position as in the Alpha Quadrant is useless to Kirk in terms of knowing when to expect help. It doesn't matter where Khitomer is in the galaxy. Sulu saying he is in the Alpha Quadrant gives Kirk absolutely no idea of when he will arrive. He could be anywhere from 5 minutes away to 5 weeks away or even further. Remember, it was originally projected to take Voyager 70 years to go from the Delta Quadrant back to the Federation in the Alpha Quadrant.
Audio problem: After Kronos One is fired upon, Kirk calls down to engineering to ask if they had been firing torpedoes. Scotty responds by looking at the inventory screen and saying "Negative Captain. According to inventory we're still fully loaded." That Scotty sure is fast. He gets through saying "Negative Captain" before his reflection even starts moving its mouth. It's a little dark so turn up the brightness on your screen. (00:28:50)
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: 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.
Visible crew/equipment: After Gorkon says, "Find Chang.", the shadow of the camera can be seen on the left side of the screen during a shot of some doors opening.
Audio problem: When Kirk and McCoy enter the underground penal colony, Kirk is confronted by a large beast speaking an alien language. Watch McCoy's mouth when he says, "He's definitely on about something, Jim." His mouth doesn't start moving until the camera shot changes halfway through the sentence. (00:59:45)
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)
Factual error: When the crew member aboard the Excelsior detects the incoming shockwave, he states, "Energy wave at 240 degrees, mark 6, port". However, when the shockwave hits the Excelsior seconds later, it is coming from her starboard side. (00:04:05)
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.
Other mistake: It was shown that whatever form Martia was in, whether it be the attractive semi-human form, the Sasquatch form, or the little girl form, her voice always remained the same. Why didn't her voice remain when she morphed into Kirk?
Audio problem: When Spock mind melds with Valeris, you hear a heartbeat. Whose heartbeat is this? It is specifically stated in the original series that Vulcan hearts beat almost twice as fast as humans. It is, however, never established that Vulcan metabolic functions slow during a mind meld, due to conscious physical control or otherwise.
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.