Continuity mistake: In the final scene on the bridge, Spock and McCoy are wearing coloured arm bands which identify their departments: Spock's is orange (for Science) and McCoy's is green (for Medical). In the very last shot, Spock is wearing the green band and McCoy is wearing the orange one (corrected in the 2022 re-release of the Director's Edition).
Continuity mistake: In the original series Spock mentioned that Vulcan has no moons. In the movie, when Spock is on Vulcan, he looks up and shields his eyes against the glare of the sun. When the scene changes, it is night and there are moons. (Corrected in the Director's Edition).
Suggested correction: Though the planet had no moons, it did form a binary pair with T'Khut and was considered its sister planet. From Memory Alpha.
Continuity mistake: (ABC Television version only) When Kirk leaves the Enterprise, you can see the set behind him. Kirk's suit also changes from the time that he is leaving the ship to the time that Spock is sent back unconscious. Unfinished scenes were added before being aired on television (corrected in the 2022 Blu-ray release of the ABC television version).
Continuity mistake: In the 2000 Director's Edition only: during the scene in which Kirk and McCoy are asking Spock why he has returned to the Enterprise, they added an effects shot of the Enterprise's warp nacelle outside the window. Keep an eye on it throughout the scene. Even considering the fact that the camera angle changes throughout the scene, the nacelle appears to "move around" (side-to-side, up-and-down, nearer/closer to the window) and the perspective/foreshortening of it never changes in relation to the camera angle. (00:53:35 - 00:56:30)
Continuity mistake: Near the end of the movie, Kirk reads the nameplate & begins to wipe off the "V-GER" sign, he uses his bare fingers to clean the sign. As he circles "V-GER" you see his hands beside them and they are perfectly clean. His hands should have shown some evidence of wiping off the VOYAGER sign.
Continuity mistake: After Spock's arrival, the Enterprise is finally able to exceed Warp 1. At the end of the test run, the shot shows the Enterprise, the beautiful light spectrum tube, and the pop/explosion created by warp speed. The problem is the pop/explosion and the spectrum tube do not line up. It's almost as if the two started at different points.
Continuity mistake: Decker's hair is parted on the left, but flips to the right when entering the wormhole, then flips back.
Continuity mistake: After Ilia is abducted by the V'Ger plasma energy beam on the bridge, her tricorder falls on the chair. The chair is facing a different angle than it was before. Also, you can see the white tips of a pair of shoes from someone standing next to the chair on the left. Presumably, this is supposed to be Kirk, but he is too far away to see his feet in that shot.
Continuity mistake: As the camera goes in on the window of the station, there is no travel pod parked at the airlock. When Kirk and Scotty go to leave, there is one conveniently there, with no announcement of arrival (Corrected in the Director's Edition. The 2022 re-release adds the travel pod to the establishing shot of the station).
Continuity mistake: When the Enterprise first leaves space dock, the deflector array is orange until warp speed, then it's blue. Inside V'Ger, it alternates from orange to blue.