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)
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: 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: After welcoming Gorkon to dinner, Kirk walks over to Spock and says "I hope you're happy". The clock behind Spock first shows 16:13:57 as Kirk is walking over, and then 16:13:55 when he reaches Spock. (00:19:20)
Continuity mistake: When Valeris advises Kirk that there is a supply of Romulan ale onboard, the clock behind her reads 16:14:08. After Kirk commends her and leaves the bridge and the camera switches to Spock, the clock reads 16:14:06. (00:19:25)
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: When Spock places the viridium patch on Kirk's shoulder, its orientation is horizontal. In the very next scene when Kirk and McCoy beam to the Klingon ship, the patch is vertical. (00:31:20)
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)
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 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: 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.
Suggested correction: The implication is that Excelsior has only very recently crossed the border from the Beta Quadrant to the Alpha Quadrant.
Even if that "implication" were true (and there's nothing dialogue-wise to indicate such) it's still useless to Kirk as to when the expect help. The dividing line between the Alpha and Beta is fully half the width of the galaxy.
Sulu doesn't expect Kirk to deduce where the Excelsior is, he tells him directly that they're unlikely to make it in time, and the reason is that they are "now in Alpha Quadrant" i.e. they were previously not in the Alpha Quadrant, i.e. they're far enough away that recently they were in a whole other quadrant of the galaxy. (I agree it's an awkward line, but it makes sense if you think of it like "I'm now in the U.S." if it's known you already live there - it means you've just returned).
Audio problem: In the original UK VHS release of the movie, during the battle sequence, Spock is lifting a panel on the floor of the bridge and says: "Auxiliary Circuits destroyed Captain." His mouth doesn't move as he's speaking.
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: 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: 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.
Suggested correction: Why is this a mistake?
Plot hole: The assassin cuts a hole in the glass to kill the Federation president. But with the size of the hole and the placement of the scope on the phaser rifle, the assassin would not have been able to see out of the hole.
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.
