Continuity: 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: 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.

Continuity: 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: 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: 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: 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.

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: 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.

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.

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.

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.

Plot hole: 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: 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.

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.

Other: Every time we see a high ranking Starfleet Officer in the Starfleet Command scenes, they are wearing dozens of different badges and medals. Why doesn't Kirk and crew have any? In just the movies, Kirk and Co. have saved Earth twice and foiled an internal assassination attempt against the Federation President. As well as all the heroic and successful missions carried out in the original series. In the classic episode "Court-Martial" it lists Kirk as recieving the Starfleet Medal of Honor, the Silver Palm with Cluster, Starfleet Citation of Conspicuous Gallantry and Kragite Order of Heroism. And it isn't because of Kirk's actions in STII and III, the military can punish you, but they don't take away previous awards and medals. And while they may not be required to wear them all the time, if there is any occasion where they would be required to wear full dress and medals, it would be a court martial - all the Starfleet officers attending Kirk and the crew's court martial are wearing their decorations.