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Audio/visual unsynchronised 

When Newt's mother is calling in the mayday, she is heard saying "Alpha zero two four niner" repeatedly, but the second time she says it her mouth is saying something else. (Special Edition only)
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When the marines and Ripley are in the Operations Room (chapter 24: 1hr 35) and the throng of aliens have burst in, there's a shot of Hicks with Gorman in the background and Gorman is shooting but no sound or gun fire is seen.
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During the ventilation shaft scene towards the end of the movie Vasquez tells Gorman "you always were an asshole". However, you do not see her lips moving at the end after the camera angle changes.
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Character error 

During the inquest, Van Leuwen refers to Ripley's company ID number as NOC14472 while the data screen in the background displays NOC14672.
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Continuity 

When Ripley tries to break the glass in the med lab there is a scuff mark on the glass before her first swing. After this finishes, the mark disappears and we see Ripley actually making the mark with her second swing.
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The first time Ripley grabs the Alien queen during the fight in the power loader, the loader's hand is closing on the queen's neck. In the next shot the hand has grasped the queen's snout.
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When Burke, Ripley and Lt. Gorman first enter the colony building, they pass through the pouring rain outside and get soaking wet. A few seconds later, inside the building, their clothes and Ripley's hair are dry again. (This scene is part of the extended edition)
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Just after finding Newt, Ripley gives her a cup of hot chocolate and the cup handle switches sides between shots.
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Near the end when Ripley is on the dropship, she is seen arming herself. We see her grab a flamethrower from the weapons rack. She then lays a pulse rifle on the deck. Next she pulls a pulse rifle from the rack, and lays down a flamethrower. (The 2010 Blu-ray is slightly re-edited to remove this error.)
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When the team first go to sub-level 3 to find the nest, the mission time in the bottom left corner of their head-cams keeps jumping backwards and forwards.
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In the elevator escape scene where Hicks gets acid sprayed, he holds his gun in front of his face and turns his head to the left. Any acid burns he got would have been to the right side of his face. As they fight to remove his melting chest armor, there are no acid marks on his face. When they leave the elevator, there are acid burns are on the left side of his head, instead of the right side.
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In the opening scene of Ripley (frozen), it shows her head tilted to her left, then the close-up shows her faced forward.
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After an alien smashes a hole through the triangular windshield on the APC during the escape from under the cooling tower the windshield is then shown with an unbroken windshield as it exits on to the planet surface.
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Towards the end, when Ripley is on her way to rescue Newt, we see the pilot light on Ripley's flamethrower. When she pauses to drop a flare there is no pilot light. The next shot shows the pilot light again.
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The first dropship has the "Bugstomper: We endanger species" logo just beneath the cockpit. During the scene where the APC rolls around the corner and is loaded onto the dropship we see the other side (pointing to the right) of the dropship and the logo faces the same way as on the pointing to the left side. In every other scene the Bigstomper logo has been correctly painted in a reverse manner it still faces toward the front end of the dropship.
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(In the extended version only) When Newt's parents explore the alien ship, there's a wide shot showing them pass through a gap in the hull. Next is an opposite shot showing them enter through the gap again.
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After the drop ship crash, after Hudson throws down the piece of debris, Hicks then grabs him and says "are you finished?". The next scene shows Hudson throwing down the same piece of debris again.
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In the scene where Burke comes into Ripley's apartment to convince her to go back in to space, Ripley lights her cigarette twice.
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When Gorman, Burke, and Ripley are discussing the firing of weapons under the primary heat exchangers as the marines are first going to sub level 3, Gorman's headset moves around on his hat, sometimes sitting below the rim of his hat and sometimes above the rim of his hat, finally toward the end it is completely under his hat.
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As the Dropship heads to the planet, Cpl. Hicks is asleep. As the ship enters the atmosphere and the marines get ready to deploy, Hicks is clearly awake. In the next shot he is still asleep. Finally Apone says "Somebody wake up Hicks." (Extended edition)
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In the previous film, when Ripley is preparing to enter hypersleep, she removes Jones from his carrier and puts him into one of the freezer tubes and closes it. Later, after disposing of the alien, she gets into the other tube; the closing shot shows her asleep with her hands resting on her abdomen. When the salvage crew enters the shuttle and finds Ripley, Jones is curled up on her stomach; he wasn't there in the closing shot - he was in the other tube.
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The monitors for each of the marines' head-mounted cameras are identified by each marine's last name and first initial, located in lower right-hand corner of the monitor (e.g., Hicks D., Apone A., Hudson W., etc.). This is true for Vasquez' monitor (Vasquez J.), with one exception. While in the processing station and after Apone says, "Uh, roger. That's a two-one-six.", her monitor reads "Vasquez.".
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Crew or equipment visible 

When Pvt. Frost gets burnt and falls to his death, you can see a cameraman's leg.
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When the team is descending down to the planet, camera lights and screens are clearly visible in the reflection off Ferro's mirrored sunglasses, and in several shots.
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Incorrectly regarded as goofs 

The Marines in the film wear (current) Army stripes - although it is likely that insignia will change in the next several hundred years, they of course do not necessarily have to.
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The shuttle pilot's seat has ejection handles. Since the shuttle travels between atmosphere & space, wouldn't ejection would be more dangerous than remaining on-board, both for the pilot AND passengers? Not necessarily so - pilot ejection would still be practical for atmospheric flight, and a sufficiently advanced seat could include a deployable bubble or shell for surviving space or even atmospheric re-entry - In the early 1960s, NASA designed a number of concepts for ejection seats that could be used to escape from a spacecraft in Earth orbit and allow an astronaut to safely re-enter the atmosphere. Passenger or payload recovery would be more problematic. But again, an integrated system of the future might provide reasonable survival capability.
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When Ripley goes back to medical to join Newt, she lays her rifle on top of the bed and then lays down on the floor beside Newt. Moments later she looks to break the glass but finds her rifle laying on a table on the other side of the glass. The scene makes it clear that Burke entered while she and Newt were asleep and laid down the opened containment cylinders with the facehuggers inside of them; it's fairly obvious that he moved her rifle out of the room as well (note Ripley's expression when she sees her rifle).
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The marines are supposed to be "Colonial Marines" but yet they have the patch of the American Flag on their uniforms (one of these patches is clearly visible on Gorman's uniform). Their full title is actually "US Colonial Marines" so an American flag would not be surprising.
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When the salvage crew shines a light onto Ripley's face while she is sleeping at the beginning of the movie, her right eyelid twitches. However, people's eyelids twitch all the time when they are asleep.
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Plot holes 

The ICC hearing had been going on for "over three hours", yet it was never mentioned once that LV426 had been colonized. This seems entirely unlikely, since this fact would be extremely relevant to the hearing. The fact that people had lived on LV426 for years and had never seen an alien would have definitely been mentioned.
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Revealing mistakes 

When Bishop saves Newt from being sucked out of the airlock, part of Lance Henriksen's real torso can be seen beneath the false one, emerging from a hole in the floor. (This error was digitally corrected for the 2010 Blu-ray release.)
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When the Alien surfaces to snatch Newt, two wires lifting its tail out of the water can be seen.
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Just before Ripley rescues Newt from the cocoon, she kills the parasite coming out of the pod and one of the aliens charges at her. As it is moving down and towards Ripley, wires can be seen on top, helping to move it along.
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When the loader falls into the airlock the wires holding it can be seen.
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When Bishop is remotely guiding the second dropship on its final approach to the landing pad, wires can be seen holding the ship on the deployable weapons pod.
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When Bishop is "doing the thing with knife" the scene is sped up to give the impression that Bishop is lightning fast. Apone can be seen rocking his head back and forth, also at a ridiculous speed.
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During the escape in the APC, containers fall from the overhead storage, yet none of them strike Gorman anywhere near his head - they later say he has a concussion, and leaves the medlab with blood from his wounds showing through his bandage. In fact, only one of the containers strikes Gorman on the right arm and they way in which they fall indicate they are empty, clearly not enough force to knock him out cold.
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When Ripley begins to torch the eggs in the chamber and the queen screams, you can clearly see that her head is not very well attached to the neck, revealing some metal parts from inside the model.
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Whilst Ferro is piloting the drop-ship down to the planetoid, on the computer screen showing navigation, the characters at the bottom of the screen are back to front, indicating that the scene had been mirrored.
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When first talking about the Pulse Rifle it is said that it uses 10mm CASE-LESS ammunition. However, in the scene in the vents, Vasquez is firing the Pulse Rifle and shell casings can clearly be seen coming from the rifle.
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Before Bishop begins doing "the thing with the knife", knife marks from earlier takes or practices are visible on the table in the exact spot where his and Hudson's hands are yet to be placed.
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During the scene in the queen's egg chamber shortly before Ripley "demonstrates" her flamethrower to the queen, an alien egg on the right of the screen, closest to Ripley's left leg, wobbles obviously. It's clearly very light and hollow.
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During the scene where Hicks shows Ripley how to use the assault rifle he unloads the magazine. The counter can be seen to remain on 42 underneath Ripley's arm while it is unloaded.
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After Spunkmeyer loads the missile, he calls "Clear behind!" and walks the power loader backward. A thick cable can be seen attached to the loader's left foot. (The loaders are supposed to be free-standing.)
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When Newt goes to bite Hicks' hand when he tries to grab her when she is first found, he clearly cries "Ow" before she can bite down.
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In two side shots of the drop ship as it passes through the clouds, a wire can be seen attached to the nose.
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The scenes showing the Marines inside the APC show that the vehicle is tall enough for them to stand upright inside of it. However, when the Marines exit the APC when inside of the atmosphere processor, it is obvious that they are quite a bit taller than the vehicle, revealing it to be a scale model.
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SPOILER:Shortly after the ship gets hurled against a pile of debris, Bishop retracts the landing ramp. The piece of debris that gets lodged into the closing ramp looks very much like a simple model placeholder for the Alien Queen, with two arms and two legs, as if the intension was to later insert a realistic looking Queen by means of a compositing effect, which obviously never came. This would be an explanation as to how the queen got on board.
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Spoilers 

The goofs below may give away important plot points.

Continuity 

When the queen grabs the loader in the final fight scene, she topples it over first smashing the yellow rotating beacon light on the top then pulling it in the airlock, but when the loader is shown in the air lock the light is undamaged and operating.
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Continuity 

After the Queen falls down the airlock, the tip of her tail has been broken off (obviously unintentional, and overlooked or not repaired by the crew.) The tip is back on moments later as she's tumbling through space.
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Continuity 

After the dropship has crashed into the APC, during his rant, Hudson throws the piece of wreckage he is holding twice.
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Revealing mistakes 

When Ripley is firing grenades into the Queen's ovipositor, after one of the last explosions, an intact, yellow chicken egg yolk is clearly seen sliding out of the wound. (It is even more obvious in one of the Quadrilogy's featurettes.)
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Revealing mistakes 

The wire that pulls the Queen's tail out of Bishop's chest is visible, but it is *not* the white strand that most people assume to be it. The strand is just an unidentified piece of material pulled out *by* the tail, and can be seen to snap and fall away. The wire itself is a monofilament visible for a brief moment before the tail begins to emerge.
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Revealing mistakes 

When Vasquez shoots the alien which causes Drake's death, the exact shot of the alien exploding and spraying its acid blood everywhere is used again when the second pair of remote sentry guns (in the special edition) are firing away. In fact, it's used twice in this scene in quick succession.
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