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- When Dallas enters MU/TH/UR, the shot from outside the interface room shows that one of the lights around the doorway is not illuminated (the fifth one down from the ceiling). In the following shot from inside the room, it is suddenly working. The exact same thing happens when Ripley enters MU/TH/UR later in the movie, meaning these two scenes must have been shot at the same time.
- Following the pull back view of the derelict, a panoramic view of the ship's landing area (with the Nostromo's lights visible through the wind-borne debris) shows the ringed planet Calpamos in the sky. However, there were no rings around Calpamos during the approach in space.
- When Dallas, Kane and Lambert are exploring the alien spacecraft, you can see that there are wipe marks inside their helmets that change between shots, most noticeably on Kane. This is because the helmets were built without sufficient exhaust systems for the actors' breath and would steam up, but in reality the characters would be unable to wipe the inside of their helmets with them on, and they couldn't possibly remove them to wipe them on LV-426 due to the inhospitable atmosphere.
- When Dallas, Lambert and Kane first discover the Pilot, the room is sufficiently illuminated for the Pilot, the device he is seated on and the surrounding floor to be perfectly visible. In all close shots, it's suddenly pitch black and all that can be seen are the small areas lit by the crew's helmet lamps.
- Kane is wearing a beige leather hood inside his space suit on LV-426. However, when his helmet is cut off aboard the Nostromo, the hood has vanished.
- When Dallas uses the pen to catch the acid blood, it melts the top of the pen to the point where it is deformed and smoking. When he hands the pen back to Brett, the top of the pen is no longer deformed at all, but it is still smoking.
- When the dead Facehugger falls onto Ripley, it lands on the floor with its legs up. The distant shot shows that its tail has looped under its body, but the close-up shows the tail laid out straight, away from its body.
- Kane's shirt changes between being tucked in and hanging out during the Chestburster scene.
- When the Chestburster erupts from Kane, the camera changes angle and there is significantly less blood on his shirt. Then when the angle changes again, the blood comes back.
- When Brett is demonstrating the cattle prod weapon for the first time, the spot he touches on the overhead has a burn mark before he touches it, likely from a prior take.
- The motion detectors used in the film often fail to pick up the movement of nearby crew members. Furthermore, the devices initially emit a high-pitched humming when they register movement, as heard when they are first tested and when Ripley, Parker and Brett mistakenly detect Jones in the locker. However, when Dallas is in the air shafts later in the film, the devices instead issue a completely different beeping tone.
- Just before Dallas is taken, he touches a patch of Xenomorph slime on the floor. In the next shot he has more slime on his hand than there was on the floor to begin with. The amount of slime on his hand also changes between shots.
- When attempting to flee from the Alien inside the air ducts, Dallas descends a ladder and is clearly not carrying his flamethrower. When he gets to the bottom of the ladder, he has it again.
- Just before Dallas is taken, Ash's headset disappears in a closeup.
- When Ripley is inside MU/TH/UR, the writing on the readout screen is projected onto her face. The screen she is looking at has four lines of green text, yet the image on her face is of one line of white text.
- Ash suddenly appears beside Ripley in the MU/TH/UR interface room even though we never heard the door (which makes an audible hissing noise) open.
- When Ripley tries to escape from Ash, she suddenly has a nosebleed for no reason. This was actually supposed to tie in to an earlier deleted scene where she suffers a decompression injury, but the sequence was cut from the film.
- The milky sweat that runs down Ash's forehead before he attacks Ripley disappears without him wiping it away.
- During Parker's fight with Ash, the sleeve on Parker's right shoulder suddenly becomes torn and a safety pin is visible holding it together. In the next shot we see his shirt intact and we see Ash tearing it.
- The positions of the various characters vary wildly from shot to shot after Ash has been beheaded.
- The items on the table behind Ash's severed head change position between shots.
- After Ash's body is incinerated, the interior walls of the Nostromo appear more metallic and grey than they were before. According to director Ridley Scott, this was done intentionally to make the Alien's presence appear more menacing.
- Parker's skin color changes in the extreme close-up of the Alien's inner jaw smashing his skull, and he also appears to be bald. The shot lasts only a split second, but the difference is still noticeable.
- The Alien's tail snakes between Lambert's feet before it kills her, but it's not her feet that are shown — Lambert wears cowboy boots, yet the feet on-screen are dressed in sneakers. The surrounding floor also changes. The shot is in fact of Brett's legs, as the footage was taken from his death scene, which was originally longer and featured the Alien lifting him up with its tail.
- In the Director's Cut scene where Brett is shown being transformed into an Egg, there is no sign of the head wound from when the Alien pierced his skull with its inner jaw.
- When Ripley is trying to set the self destruct aboard the Nostromo, the sequence begins before she activates the fourth and final button on the control panel.
- The rods that rise up out of the self destruct mechanism switch between being up and down from shot to shot when Ripley tries to deactivate the countdown.
- After Ripley fails to cancel the self destruct we see a shot of the countdown clock showing about 4 minutes 50 seconds left to destruction. Following a shot of Ripley, there is another quick shot of the countdown clock, now showing 10 minutes 39 seconds left to destruction, even though detonation was supposed to happen just 10 minutes after the countdown was first initiated.
- MU/TH/UR's two 30 second countdowns take 36 and 37 seconds respectively.
- It can be seen multiple times throughout the film's final act that Jones is not in the carry box. This is most obvious when the front or back of the box is toward the camera when Ripley is moving through the corridors.
- When Ripley backs into the shuttle's closet there are three axes on the wall next to her. When she starts to get into the space suit there are only two, then when she puts the helmet on there is only one.
- The two "knobs" on the front of the space suit helmet Ripley wears are sealed when she is inside the locker, but when she is in the shuttle's cabin the knobs are open at the bottom.
- In the shuttle, Ripley presses buttons to release steam or gas onto the Alien. During the first two bursts of steam (which miss the Alien), the inside of her helmet is foggy and streaked. After the Alien reacts to the third blast of steam, the inside of Ripley's helmet is suddenly clear.
- When Ripley shoots the Alien with the harpoon gun, its acidic blood should quickly melt the harpoon and/or its cable, releasing the creature, yet it does not.
- A dippy bird is seen on the table in the mess hall throughout the film. Dippy birds require water to drink, otherwise they will not move. However, the bird is moving when the crew first wakes up, even though they have evidently been asleep for some time (they are in an unknown part of deep space, 10 months away from Earth). As a result, any water in the beaker should have evaporated a long time ago and the bird should be motionless.
- Several times in the film, the data being shown on computer screens is seen projected onto the faces of the crew. It would be impossible to read a screen that bright.
- MU/TH/UR issues several basic grammatical/spelling errors throughout the film. When Dallas first queries her at the start of the film, "ALIGNMENT" is misspelled "ALLIGNMENT". Later, the computer states Special Order 937 is to "INSURE" the safe return of the organism. The correct verb would be "ENSURE". Also, messages typed by the crew are supposed to be underlined, while messages from MU/TH/UR are not. However, this arrangement goes awry.
- In the Director's Cut, LV-426 is said to be 1,200 km in diameter and have a surface gravity of 0.86 G. For a moon that small to have a gravity of 0.86 G, it would have to be made entirely of a materiel more than twice as dense as the densest element known to man, osmium. Its surface would also be visibly curved when standing on the ground, which it clearly is not.
- One of the moons in the system containing LV-426 is out of phase with the others.
- During the landing sequence, Kane issues the instruction, "Roll 92 degrees port yaw." Roll and yaw are two entirely different directional axes in flight and would never be combined.
- When the crew ejects Kane's body into space, it begins to flip faster and faster as it moves away from the ship. Such an increase in rotation could only be caused by aerodynamics. However, there is no atmosphere in space, and as such aerodynamics do not exist there. As a result, Kane's body should rotate at a constant velocity after being shot out of the airlock.
- During the introductory external shots of the Nostromo, the stars in the background remain constant, even when the Nostromo and its cargo are shown from different angles, indicating the same backdrop was used.
- At the start of the film when the cockpit is shown for the first time, you can see the camera shake as it bumps into something whilst it pans towards the seats. The sound of the bump can be heard as well.
- When Dallas first interfaces with MU/TH/UR, he says, "Good morning, Mother." However, the voice does not sound like Tom Skerritt's.
- When the acid is burning through the Nostromo's decks, the same shot of the blood burning through from above is used three times.
- When the crew are watching the acid eat through the decks of the ship, Parker says, "Take a look at this, man!" However, the movement of his lips does not match his words.
- Just before the dead Facehugger falls on Ripley, the collar of her outfit begins to pull downward, unnaturally, until the Facehugger drops onto her shoulder. There was likely some sort of filament, fed from below, running through her clothing and attached to the Facehugger, that was used to pull the creature down onto her.
- When the crew are dining together just before the Chestburster scene, the scene cuts from a long shot, where Parker is saying something, to a closer shot, with the conversation continuing as before. Parker's voice can still be heard, but his lips are no longer moving in the second shot.
- Following the Chestburster scene, as the camera pans around the darkened corridors just prior to Dallas ejecting Kane's body, what appears to be a boom mic is visible for approximately two seconds to the left of the screen.
- The wires holding up the Alien as it drops down behind Brett are visible.
- When Dallas is crawling through the air ducts before he is taken by the Alien, you can see dolly tracks for the camera along the floor.
- When Parker beats Ash with the fire extinguisher, the prop bends back and forth.
- After Lambert hits Ash with the electric prod, the camera pans down and we can see wires on the ground leading to the prop Ash torso atop Parker. The figure Parker is wrestling with is also just a mannequin of a torso and has no legs connected to it.
- When Ripley reconnects Ash, the switch from dummy to actor is blatantly visible. When the android is incinerated, the switch back to the dummy head is equally noticeable, and Ash's left arm also disappears. Furthermore, as Ash burns, his face melts off, revealing a solid dummy head beneath with no eyes and a sealed mouth.
- When trying to abort the self destruct, the cancellation instructions Ripley follows with her finger are actually just a French translation of the detonation instructions she followed earlier.
- After failing to shut down the self destruct, Ripley runs through a corridor filled with venting gas. As she steps out of the gas, the arm and head of a crew member is clearly visible near the large light. This is acknowledged on the DVD commentary.
- When Ripley is in the shuttle and has the space suit on, she hits the button to open the door and blow the Alien into space. In the shot just as the Alien is getting sucked backwards, the wire coming out of its back that pulls it is visible.