(at around 21 mins) 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)
During the scene in Ripley's apartment, where Burke is trying to convince her to go with them, Burke (Paul Reiser) calls Ripley (Sigourney Weaver) by her real name (or rather a shortened version of it):
"Sig; these colonial marines are very tough hombres."
(at around 1h 45 mins) 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, the acid burns are on the left side of his head, instead of the right side.
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.
In Alien, the computer displays have an old-fashioned "teletype" clicking noise when they show data on their screens. However, when the screen in the Nostromo shuttle comes to life at the beginning of Aliens, the display looks and sounds more modern like the other computer screens seen later in the film - even though 57 years have passed and the equipment in the shuttle has not been touched all that time.
The first dropship has the "Bugstomper: We endanger species" logo just beneath the cockpit. When 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.
(at around 54 mins) 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.".
When the Marines and Ripley first encounter Newt, Drake fires wildly at Newt's scurrying silhouette as Hicks uses his own pulse rifle to deflect Drake's line of fire up and into the corridor wall. But there is no visible damage to the wall after Drakes ceases firing.
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)
When Hicks first gives Ripley the locator wristband, the locator can be heard beeping at a steady rate. However, near the end of the film when Ripley finds the wristband while trying to rescue Newt. The locator beeps much faster, even though the wristband is about the same distance away as it was in the Ripley/Hicks scene earlier.
(at around 1h 5 mins) When Vasquez shoots the alien that suddenly comes out of hiding near Drake as the Marines are escaping the processing plant, its blood splashes across his entire body, but only the left side of his body is shown as being affected.
(at around 53 mins) 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)
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.)
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.
(at around 3 mins) In the very beginning of the movie when the salvage crew is cutting into the lifeboat, in the close-up shot the plasma cutter makes a cut at a right angle but in the long shot when the door falls, there are no right angles on the door they cut. So the shape of the door being cut does not match between the close-up and long shots.
(at around 1h 2 mins) When the ammo bag that Frost had been holding explode, Crowe is thrown against a wall, breaking his neck, yet Hicks reports that "Wierzbowski and Crowe are down". He should have said "Crowe and Frost are down", as Wierzbowski is still alive at this point.
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.
(at around 56 mins) 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.
(at around 26 mins) 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.)
When the dropship is released, it is shown to be falling immediately as if in full gravity. However, since the Sulaco is placed on a stationary orbit, the dropship should remain in place upon releasing the clamps. An additional burn would be necessary to initiate deorbiting.
At the end of the movie, the compound explodes and the survivors escape in a shuttle. We see that brightness of the explosion shines on their face. But in fact, the explosion and the light source is behind, so there's no way their sight would be affected by the brightness.
When the drop-ship is lowered into the airlock, it is held in place by a number of arms lowering it from the ceiling. Presumably the inner airlock doors close round these arms, which continue to hold it prior to release. However the outer airlock doors open below the ship just a few seconds later, without enough time for the airlock to have been evacuated to anything close to a vacuum.
The landing sequence is incorrect. The dropship is seen accelerating while deorbiting, such acceleration would send it to a higher orbit. Deorbiting needs deceleration from the orbital speed. The dropship should have fired retro-rockets or it should have turned backwards to use the main thrusters for deceleration.
Moreover, if the Sulaco is exactly above the colony (as stated in the novelization), the dropship should have done a vertical drop (relative to the planet) or should have completed a full orbit while descending to end up right above the colony.
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. According to the Aliens VS Predator universe, the United States as we know it right now has evolved by the time of the movie (assuming that the movie is in the AVP universe), it's known as the "United Americas", so the American Flag patch on the Marines' uniforms makes no sense as is Burke and Bishop mentioning some American States (i.e., Wisconsin and Nebraska respectively).
(at around 1h 29 mins) 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).
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.
(at around 4 mins) 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.
(at around 2h 10 mins) At the end of the film as Ripley is closing the sleep chamber for Bishop, you can clearly see his IV pack has an expiration date of 08/87. However, Aliens takes place in 2179, so the expiry date could be 07/2187.
When Hudson tries to locate signals from the colonists' personal data transmitters, he initially gets no readings. However, Newt, who as a colonist should have a transmitter implanted, is sitting only a short distance away.
The inquest had gone in for "three and a half hours", yet no one had mentioned that LV426 had been colonized for over twenty years? One would think that would be one of Van Leuwen's first responses to Ripley's claim the planet had hostile Aliens on it.
Corporal Hicks gives Ripley a wristband that has a tracker in it. Hicks can always find her with the locator that he has. Later Ripley gives this to Newt but does not tell anyone. Near the end of the movie Newt slides down a shoot and Corporal Hicks excitingly exclaims "We can find her with this" and holds up his locator, but he shouldn't know that Newt has the wristband.
Although the marines' scanners can pinpoint individual aliens through walls, they (inexplicably) cannot tell if those aliens are on the same level, above, or below the marines. Even if the scanners were only able to operate in two dimensions, simply turning the scanner 90 degrees would make their vertical position obvious, and yet none of the characters does this. The aliens' ability to surprise and slaughter the marines half way through the film hinges entirely on this artificial limitation.
(at around 21 mins) 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.
(at around 1h 25 mins) After Vasquez cuts a hole in the conduit to allow Bishop to crawl to the transmitter, the metal cut out segment falls into the conduit pipe through the hole. However, a few moments later after Bishop has entered the pipe, Vasquez replaces the cut out piece and it does not fall through.
(at around 1h 6 mins) 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.
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.
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.
(at around 21 mins) 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.
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.
(at around 1h 45 mins) When Ripley is preparing the M41 rifle with the flamethrower she is seen loading a new cartridge of ammo in the rifle as the counter runs up to 95. Once the elevator doors open the counter reads 42. She hasn't yet fired a shot.
Just before Ripley rescues Newt from the cocoon, she kills the parasite coming out of the egg 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.
The goof items below may give away important plot points.
In the final scene when the survivors are preparing for hypersleep, there is an I.V. bag of "Sodium Chloride" solution by Bishop's head, milky white like the android's blood, not clear like a human's saline solution would be, with a printed date of "Expiry 07/87", the year after the movie was released. (Although according to the Alien Universe Timeline, Aliens takes place in 2179, so the expiry date could be 07/2187.)
After the first contact with the Aliens at the processing station and Drake is killed, Vasquez is being held back by Hicks near the door of the APC. He yells that Drake is gone and she says, "No he's not," but her mouth does not move in sync with the line.
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.
(at around 2h 10 mins) After the Queen falls down the airlock, the sharp end of her tail is missing (obviously unintentional, and overlooked or not repaired by the crew). The tip is back on moments later as she's tumbling through space.
When Newt's parents enter the derelict ship, they don't have any descending gear so it is not clear how the man got facehugged as in Alien, as the eggs are in a chamber deep below the entrance level, inaccessible without some descending equipment.
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. (James Cameron acknowledges this error on the DVD commentary; the goof was digitally corrected for the 2010 Blu-ray release.)
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.
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 DVD featurettes.)
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.