- Audio/visual unsynchronized: When Madison and Taggart are standing at the start of the chompers, the audio track has Madison saying "Screw this!" However, looking at the visual, she is clearly using another expletive instead of "screw". Apparently, this overdub was necessary to maintain the PG rating from MPAA.
- Continuity: When Tech Sergeant Chen is helping to roll the beryllium sphere on the planet, he is shown holding a large brown paper bag with his teeth. A split second later, the bag is gone.
- Continuity: 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.
- Continuity: The number of earrings in Sarris' left ear throughout the movie and especially within several scenes that are only seconds apart.
- Audio/visual unsynchronized: 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".
- Incorrectly regarded as goofs: In the credits for "Galaxy Quest: The Journey Continues," the credits read "Jason Nesmith as Commander Peter Quincy Taggert", though it's consistently spelled "Taggart" in many other places. This is an example of the cheesiness of that show.
- Continuity: 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.
- Continuity: 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.
- Continuity: 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).
- Continuity: When Laredo/Tommy Webber is starting to take the Protector out of the space dock initially the computer is on, then a few seconds later it goes off, and then goes on again.
- Crew or equipment visible: When the actors are returning to the shuttle with the sphere, in a long shot, tents are visible in the background.
- Factual errors: On the original 2000/2001 DVD cast and crew listing, Justin Long is mistakenly billed as Brandon Long (Brandon being the first name of his character in the film). On the 2003 DVD cast and crew listing, he is correctly referred to as Justin Long.
- Continuity: 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.
- Continuity: When Tommy is taking the Protector out of the space dock, he scrapes the hull along the side of the dock, but the port engine should be in the way.
- Revealing mistakes: When talking to Jason Nesmith about the Omega 13, just before he takes him over to Mathesar to admit he is an actor, Sarris leans his head back and you can clearly see the actors teeth behind the Sarris mask.
- Audio/visual unsynchronized: 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.
- Continuity: When Taggart is first "abducted," his limousine initially shows no front license plate. However, in a subsequent shot it has a California plate.
- Continuity: 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.
- Factual errors: 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.
- Continuity: 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.
- Anachronisms: Scenes depicting the fictional Galaxy Quest TV show employ (deliberately poor) CGI in the SFX shots. However, in the time the show was supposedly aired (1978-1982), scale models were used for such scenes instead of CGI (interestingly, Tim Allen's character does say the NSEA Protector is a tiny model, but scenes of the Galaxy Quest show clearly use CGI and not models).
- Continuity: When Alexander is being introduced, he bows with his hand flat against his chest. When he comes up, his hand is in a fist.
- Continuity: 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.
- Continuity: When talking about the digital conveyor, Tommy pushes Tech Sgt. Chen forward, then disappears seconds later.
- Continuity: When Sarris enters the deck the first time disguised as Fred, he enters after Alex is finished speaking. After the Omega 13 is activated, Sarris enters while Alex is still speaking.
- Continuity: The first time Sarris enters disguised as Fred, his arms are at his sides an he reaches for his gun. The second time, his right arm is behind him holding the gun.
- Continuity: When the good guys 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 Saris and crew entering through the open door. When the camera cuts back to the good guys, they are now walking toward the door, apparently unaware that anything is happening, and they are surprised all over again at the appearance of Saris.
- Incorrectly regarded as goofs: The Thermians claim they are completely unfamiliar with the concept of deception, yet they have appearance generators. However, these appearance generators are not used for the purpose of deception; they are used to make things easier on the human crew. This is clearly indicated in the scene where the Thermians forgot to turn on the devices. Once they remember, it's obvious they know their actual appearance is very distressing to the humans.
- Continuity: 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 parameter.
- Audio/visual unsynchronized: When Jason is fighting the pig lizard, you can hear him talking into the communicator. However, the video of him shows that he is clearly flailing both arms about.
- Plot holes: Commander Nesmith admits during the mess hall sequence that the crew found the Omega 13 in the original show and that 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.
- Audio/visual unsynchronized: When DeMarco and Taggart come upon the "chompers" Weaver is heard to say "well screw that!" but her lips clearly use another expletive. Must have been trying for a lower rating.
- Errors made by characters (possibly deliberate errors by the filmmakers): When Taggart says the ship is a little model "about this big", he indicates a size between thumb and forefinger. Miniatures in movies and TV tended to be fairly large - large enough for all the wiring for the lights and a fair amount of detail.
- Errors made by characters (possibly deliberate errors by the filmmakers): When Jason tells Gwen to mute the audio so Sarris cannot hear him, she tells him she didn't do it because she doesn't know where the mute button is on her console. A recurring theme throughout the entire movie is that the NSEA Protector 2 and all its instruments were designed by the Thermians based on their observations of the crew's actions from the TV series, hence why Tommy said his piloting terminal was very familiar, since he remembered it from the show. In this respect, Gwen should've been just as equally familiar with her terminal, since it was the same as the fake one from the show, and therefore should know how to mute the audio, but in the scene she does not know how to do so.
- Factual errors: Although Kwan is supposed to be playing a character of Chinese ancestry, it is very obvious that he is not of Chinese descent.
- Errors made by characters (possibly deliberate errors by the filmmakers): During the phone conversation between Gwen and Alexander, Alexander is still wearing the Dr. Lazarus headpiece. Later in the film, we see hair sticking through the headpiece, so there is clearly no reason why he would still wear it at home.
>>> WARNING: Here Be Spoilers <<<
Goofs below here contain information that may give away important plot points. You may not want to read any further if you've not already seen this title.
- Errors made by characters (possibly deliberate errors by the filmmakers): SPOILER: After Nesmith kills Sarris and the crowd goes wild, you can hear the announcer yelling in the background over the cheering, "Peter Quincy Adams" instead of "Peter Quincy Taggart".
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