When Lt. Ilia is abducted from the Enterprise bridge by V'ger, a computer voice is heard on the bridge repeating the phrase "Negative control at the helm". However, Lt. Ilia's was the ship's Navigator and it was Mr. Sulu who was the Enterprise's helmsman. As he (Mr. Sulu) was sitting at the correct station, it was the Navigator position which was left vacant by Lt. Ilia's disappearance. Subsequently, Kirk then asks Decker to have another officer "Take the Navigator's position" and when Chief DiFalco arrives on the bridge, she is then instructed to take the Navigator station.
Edna Glover's scene as the Vulcan Kholinahr Master was filmed with her speaking English. Only later were Vulcan words (invented by James Doohan) recorded over the original dialogue. The phonetics of the Vulcan words were chosen to closely follow the original English script so that her lips would seem to move correctly, and English subtitles were inserted with the phrasing reworded so the change would not be obvious. For example, when the subtitles say "Our ancestors cast out their animal passions on these very sands" her lips are clearly saying "Spock, on these sands our ancestors cast out their animal passions." Other examples are "Your thoughts... give them to me" [subtitle] versus "Spock... give me your thoughts" [actual] and "Your human blood is touched by it, Spock" [subtitle] versus "It stirs your human half, Spock" [actual].
When the Vulcan Master (Edna Glover) performs a mind meld with Spock during his Kolinahr ceremony, her face drops with obvious disappointment when she learns of the space consciousness calling Spock which is clearly an emotion a Vulcan Master shouldn't be feeling. She also beams with obvious pride earlier while talking about Kolinahr as "total logic".
In several shots of the Enterprise throughout, we plainly see a pair of phaser turrets just below "U.S.S. Enterprise" on top of the saucer section. As Kirk, Spock, McCoy, Decker and Ilia emerge from the saucer section en route to their V'Ger encounter, the phaser turrets are completely missing. Not only this, the slope of the hull is far too steep. (this is fixed on the Director's Edition DVD).
When Spock ejects his thruster pack during the space walk, the initial shot from behind shows it rotating counterclockwise and moving to Spock's right. There is an immediate cut to a shot from in front of Spock, and the thruster pack can be seen in the background to Spock's right (POV left), rotating counterclockwise from this angle as well.
In the original version, Spock's first scene shows him squinting into bright sunshine - preceded by a reverse shot showing a dark sky. This error is corrected in the Director's Edition, with a new landscape and sky on Vulcan.
As the travel pod flies by to dock with Enterprise, it is shown passing in front of a light beam that was pointing at the Enterprise's warp drive section. When the travel pod passes in front of the beam, it is lighted. However, there should have been a shadow on the Enterprise when the transporter passed by.
AS we look through the window of the Floating Office Complex from the outside, there is no Travel Pod docked in the dock (next to the window). Moments later, after Admiral Kirk beams aboard, he and Scotty enter a Travel Pod docked at that dock.
As the bridge crew is watching the orifice beginning to open from the view screen, a quick cut from behind the Enterprise shows the orifice still completely closed. Most evident from bright light emanating beyond the opening in the bridge scene.
After the shot of Kirk's shuttle tram flying past the Golden Gate Bridge, there is a shot of the United Federation of Planets logo. During this shot, stage lights are reflected on the floor. (1979 Version only)
When the Enterprise moves out of the spacedock, the bracing used to hold the model can be seen silhouetted against the spacedock on the Starboard side of the ship. This has been corrected in the Director's Edition.
As Kirk exits the shuttle at Starfleet Headquarters, immediately before he first sees Commander Sonak, a male crew member with regular 20th-century clothes is very quickly visible near the back of the shuttle next to a blonde female extra before both are obscured by Sonak's entry doorway (the extra begins her own walk-through in the background once Kirk and Sonak begin speaking).
In the Director's Edition, when Admiral Kirk's air tram shuttle approaches Starfleet Command in San Francisco, it is seen heading for a building at least a hundred feet up from the water (this is an all new scene, which never appeared in the theatrical version). Yet when we see this scene from the other side, that same building appears to be level with the water's edge.
In the Director's Edition, during the "Please sit down" scene with Kirk, Spock and McCoy, the starboard nacelle is visible outside the window. But the stars are "moving" port-to-starboard, against the perspective of the nacelle. They should be "moving" starboard-to-port.
When Kirk rescues Spock during the spacewalk outside of the entrance to V'ger, an unconscious Spock is floating towards Kirk who catches him. They remain stationary thereafter. This would not happen in the depicted environment. With nothing to keep Kirk in place, they should both move away, at reduced speed based on their relative masses, after Kirk catches Spock.
When Kirk first comes on board Enterprise he is called "Admiral," and then "Captain" a few seconds later. However, it is customary for the person in command of a ship to be addressed as "Captain," regardless of his military rank.
Near the beginning of the movie Kirk tells Scotty "...an alien object of unbelievable destructive power is less than three days away from this planet (Earth). The only starship interception range is the Enterprise." While this is of course important for the whole plot of the movie and the reason why the Enterprise should intercept V'ger, it is highly unlikely that in generally and also especially in a time with war conditions with for example the Klingon Empire there is no protective fleet (not one ship apparently) inside the Solar System or within a 3-days-journey of it.
When Spock is doing his EVA into the interior of V-GER, the reflection we see in the visor of his spacesuit helmet should be the reverse of the image we see when looking over his shoulder, yet they are the same.
When the V'Ger probe first comes onto the bridge, the portion of the set around the probe appears to "shrink". For example, the view screen is not as wide in one shot, and the dome in the bridge ceiling disappears and reappears as the probe passes in front of the helm and navigation console. This was due to a distortion effect, done to "hide" the electrician holding the light source used in this sequence.
When the USS Enterprise is seen leaving spacedock bound for Vger, the Earth is shown in the background as the sun slowly rises behind it. Since this appears to be a stationary camera facing towards the ship, it should not be possible that the sun can be seen 'rising up at dawn' from this position in outer space. Only an observer on Earth or a camera leaving earths gravity would see this view of the sunrise.
When Spock puts the nerve pinch on the man in charge of the suit lockers, the thruster suits in the lockers are those intended to be worn for the original Memory Wall sequence that would have followed this scene originally. The suits worn by Spock and Captain Kirk later on in the movie are of a very different design and have a larger helmet.
The goof items below may give away important plot points.
The entire twist of the plot centers around "V-Ger" actually being "Voyager," as demonstrated by the corroded name plate on the Voyager probe. We are left to assume that nowhere in its programming (or anywhere else) did Voyager have its name recorded and that the advanced computer race was unable to scrape off the carbon scoring on the name plate.