McCoy: Well Jim, I hear Chapel's an M.D. now. So I'm gonna need a top nurse, not some doctor who'll argue every little diagnosis with me. And they probably re-designed the whole sickbay, too. I know engineers, they LOVE to change things.
If you look at the Kholinar necklace Spock was to be given when he was on Vulcan it bears a striking resemblance to the Enterprise, especially when it is laying on the ground before Spock picks it up. See more...
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Continuity: This is only in the original version of the movie. 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. This has been corrected in the new version.
Continuity: 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.
Continuity: 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: 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.