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: 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).
Revealing mistake: When the Enterprise is leaving its docking station and pulling out, two little bugs or debris from the model lands on the camera lens on the lower left corner (corrected in 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.
Revealing mistake: The shot of the Enterprise finally clearing free of the dry-dock shows a supporting pylon protruding from the starboard side of the engineering section of the starship miniature. (Corrected in the Director's Edition).
Revealing mistake: When Spock's shuttle is lining up to dock with the Enterprise, look below the shuttle and you can see the hydraulic mechanism used to maneuver it.
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: When V'Ger first appears on the bridge as a column of light, you can see that the two sides of the image don't match up, because they tried to splice the special effects person who was moving the column out of the shot.
Revealing mistake: As the pod carrying Kirk and Scotty aligns itself to dock with the Enterprise, a ghost-image of the support stand for the miniature can be seen following the model beneath it.
Visible crew/equipment: When the four officers and Ilia exit the ship onto the hull and begin walking towards the V-ger structure, the outline of the hole left in the matte painting of the Enterprise saucer section is visible. (Corrected in the Director's Edition).
Revealing mistake: When Spock is on Vulcan, it is blatantly obvious the actors playing the Vulcan elders are speaking English with a bad dubbing.
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.
Factual error: In between the scenes when they are leaving Earth and passing through the Jupiter system, you can see stars flying by on the viewer. How could they be flying by stars if they haven't even left the Solar System?
Other mistake: When the robotic Ilya punches her way out of sick bay, the edges of the hole should be pointed outward, and there should be debris on the floor. There is no debris, and the edges are pointing inward.
Factual error: Right before Epsilon XI gets vaporized by V'Ger, Lieutenant Commander Branch (the person talking during the transmission seen during the meeting on the Recreation Deck) states that V'Ger is 82 AU's in diameter. Something that big would not even fit in our solar system, as 82 AU's is about 2.7 times the distance Neptune is from the Sun (corrected in the Director's Edition).
Revealing mistake: As Pod 5 goes over the Enterprise in the Inspection cruise so Kirk can see the refit results, as the camera looks toward the Earth and the nacelles, you can see the blue of Earth through the inside of the nacelle.
Continuity mistake: Decker's hair is parted on the left, but flips to the right when entering the wormhole, then flips back.
Revealing mistake: As the ship gets close to the camera leaving space dock, you can see the interior lights of the model through the torpedo launcher opening.
Revealing mistake: After leaving space dock, the Enterprise is shown flying by the camera. As it does, there is a shaft of blue light directly underneath the ship. This can only be a poorly disguised pole under the model. (Corrected in the Director's Edition.)
