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 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.
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 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.
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 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.
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.
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 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 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.
While fighting the rock creature, Taggart loses his shirt before being thrown far away from it. After he is digitized to the ship, someone hands him a shirt and it is the same one that he left on the planet.
When the crew approach the surface of the planet in order to land, a crescent moon is visible in the sky. However the crescent shows that the light is coming from ahead and to the left, whilst the shadows on the planet are from a sun which is over to the right.
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. This is, in fact, a reference to non-Caucasian characters often being portrayed by Caucasian actors throughout much the history of Hollywood.
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. However, Brandon and his crew, as well as others have, apparently, had extensive discussions of the device and its nature, indicating the device had been discussed in TV show episode(s) of Galaxy Quest, at least hinting to its nature. The Thermians would have seen the same episode(s), and with their advanced technology, may have developed theories similar to Brandon's. Nesmith "not knowing" what Omega 13 does, does not exclude Commander Taggart from suspecting or having discussed what it may do during the TV show. Also, not knowing what a device does, does not exclude discussion of its composition, which would have been duplicated to exact detail by the Thermians.
When Nesmith is explaining to Mathesar that they are actors from a show he says, "There is no Captain Taggart." In a following line he uses the correct "Commander Taggart" title. While this is not consistent with previous and later dialog, it is not incorrect. An officer's rank is not exclusive of his duty title. The commander of a vessel with a crew may be appropriately addressed by his rank, or as "Captain", regardless of his actual rank or frequency of use of either.
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. During "episode 81" of the original Galaxy Quest TV show, Guy Fleegman played "Crewman #6", as he states to Nesmith before departing the shuttle on the surface. In the Galaxy Quest movie, Sam Rockwell plays the character "Guy Fleegman", and is called "Guy" by the other Galaxy Quest TV show actors during the movie. It would not be unusual for Nesmith to know Guy's last name, and refer to him by that name, even if he didn't recall it earlier. Commander Taggart likely addressed him simply as "Crewman", or not at all, as it was scripted for the TV show. For most of the Galaxy Quest movie, the Galaxy Quest TV show actors refer to one another by their actual (movie) names, rather than their TV show character names. Guy Fleegman's original TV show character not only did not have a last name, he didn't have a first. This would not be uncommon for such a production, as lesser characters in similar productions are simply addressed by their title, followed by a last name, or simply their title, such as "Crewman". This is true for many productions, especially when that "crewman" is "killed" during an episode, as Fleegman says occurred "before the first commercial in episode 81" of the Galaxy Quest TV show. Additionally, "Guy Fleegman" is introduced as "Security Chief 'Roc' Ingersol", during the Galaxy Quest: The Journey Continues credits.
Sarris' original interest in the "Protector" is the Omega 13, but after he captures the ship, he plans to blow it up without taking the device, despite the fact that everything on the ship works. However, at this point Nesmith has explained that it was a TV show and that the actors don't know what the Omega 13 does, so even though everything else on the ship works, Sarris no longer believes that the Omega 13 is real.
Fred advises Nesmith the beryllium sphere is damaged after their first battle with Sarris. Nesmith then explains to Mathesar that they only know the sphere as made of "wire and plaster", as it was used on the set of the Galaxy Quest TV show. It is too convenient that when they need a replacement beryllium sphere, they are found on a planet very distant from Earth, and they appear and function exactly as they were scripted and created for the TV show. The only explanation is that someone within the original TV show cast or crew is in fact, an extraterrestrial who possessed knowledge of such exotic alien technology.
When the "crew" first arrives on the Protector, Mathesar tells them he does not believe there is a man, woman or child on his planet that does not know who they are (implying their own planet remains occupied). But later he tells them he and his fellow Thermians on the ship are "all that are left", therefore returning to their home world would be pointless.
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.