When Madison and Taggart are standing at the start of the chompers, the audio track has Madison saying "Screw this!" However, she is clearly saying "Fuck this!" but was dubbed for the PG rating from MPAA.
At the beginning of the movie, after Jason Nesmith enters the dressing room of the convention center, the audio track has Tommy Weber (Laredo) saying, "You are so full of it, man!" However, looking at the visual, he is clearly using another expletive instead of "it". This overdub was necessary in order to obtain a PG rating from the MPAA.
When the two teenagers are entering and leaving the restroom they are talking and laughing. At some moments you can see their mouths but they're not moving even though you can still hear them talking and laughing.
At the convention, when Guy Fleegman is about to introduce Jason Nesmith, the backing band's only guitar player can be heard playing a simple 8th note pattern. Yet this very musician can be seen in the frame to the far right side, doing nothing.
During the Galaxy Quest convention at the beginning of the movie, Tommy Webber is introduced as "Crack gunner, 'Laredo'...Tommy Webber!" However, it is demonstrated throughout the movie (and in clips of the original Galaxy Quest TV show) that Laredo is the ship's helmsman, not the gunner. The role of helmsman also fits with his character's catchphrase of, "Pedal to the metal, Commander!"
When Nesmith and DeMarco are in the engineering room aborting
the self-destruct sequence, DeMarco's uniform goes from being zipped up before they press the blue button, to being unzipped immediately afterward (the scene has been edited to remove a segment where DeMarco seduces one of Sarris' soldiers).
When the actors are busy signing autographs at the convention, Alexander Dane swiftly brushes off two Lazarus impersonators. However, in the shot immediately before this, you can see the two fans in question already leaving the table with their autographed photographs.
As the characters bow on stage at the end of the movie, Gwen Demarco's feet are side-by-side in the front shot, but when the camera angle changes to a rear view, she has her right foot crossed behind her left.
When Commander Taggart is signing autographs for a bunch of teenage Questrians, there is a girl at the end of the table. In the next shot, she is gone, and in the next shot, she is in the middle of the bunch.
When Brandon and his crew approach Jason Nesmith at the autograph table, Katelyn (blond girl in red/gray uniform) is standing on Brandon's right side. When Nesmith stands up, Katelyn is suddenly standing behind and to the left of Brandon.
Near the end, when Nesmith/Taggart goes to activate the Omega 13, he places his palm on the button (so far that he moves the levers on the side of the button). But in the very next shot, from the front, his hand is still hovering over the button.
Sarris and Jason have their ships going head to head. Jason calls for Mark 4 speed and the exterior shot of the ship shows nothing behind it. When Jason reveals to Sarris that he's "dragging mines" the exterior shot now shows mines right on the ship's tail.
At the Tech Value Electronics Superstore, Alexander has 3 silver rectangular bars on his right collar. But when they are signing autographs immediately after, they are gone. Later, when they are in the air, the bars are back.
When our heroes are in the engineering room, unable to raise the command deck on the intercom, they hear the doors to the room open, and they all look up in surprise. Next we see Sarris and crew entering through the open door. When the camera cuts back to our crew, they are now walking toward the door, apparently unaware that anything is happening, and they are surprised all over again at the appearance of Sarris.
When the shuttle lands on the mining planet, we see a crescent moon lighted from the left, but the shadows of the rocks show that the landscape is lighted from the right. Even if this is a planet of a double star, the moon should have a crescent on the right side.
Although Kwan is supposed to be playing a character of Chinese ancestry, it is very obvious that he is not of Chinese descent. However, during the rock monster scene, he says that "Kwan" is not his real name.
On the way down to the planet to get the beryllium sphere, Guy says no one knows his last name. Up till this point in the film his last name isn't mentioned. On the planet when hatching their plan, Jason calls him "Fleegman" and tells him to set up a perimeter.
Commander Nesmith admits in the mess hall that while the crew found the Omega 13 in the original show, they had no idea what it did when activated. Unless specifics of the Omega 13 were discussed in the original show, it is highly unlikely that the Thermians would have been able to replicate it on the Protector II since it was such a foreign, mysterious object.
When Tommy is first pulling the ship out of the station he scrapes the front of the ship. The way the wings project out on each side of the ship, the left wing should have also scraped the sides of the launch tunnel too, but it comes out unscathed.
At the end, when the actors are taking their bows at the convention, as they bow Gwen DeMarco bends a knee but does not cross her legs. When the camera shifts to a rear shot, her legs are crossed for the bow.