In the scene where Ripley reconnects the dismembered Ash droid, the switch from dummy to actor is blatantly visible. A few minutes later the android is incinerated, at which point the dummy head has reappeared and the android's left arm has disappeared.
During the alien chest-burster/death of Kane sequence, Kane's shirt switches back and forth from being tucked-in, to being un-tucked throughout the scene.
In the rapid closeup sequence in which the alien kills Parker (Yaphet Kotto) by biting him right in the face, a freeze-frame viewing indicates that, at the point of impact, a honeydew melon was used to absorb the bite. Now a honeydew melon has a white external rind, and Kotto is a black actor. Why couldn't the SFX guys, at least, have painted the melon to match Kotto's complexion? This production error is, well, in your face.
When the search party goes into the boneship, they are wearing full space suits, and hoods under their helmets. When Kane's helmet is first cut off, he has no hood on.
In the scene where Lambert deactivates Ash by using a cattleprod, you will notice that she is wearing brown cowboy boots. Minutes later as the Alien goes to wrap its tail round the back of her legs, she is now wearing a sneaker - though you only see the toe cap it clearly not a brown cowboy boot.
While the Alien is bursting out of Kane's chest, notice how the blood stain on his shirt changes in size from a large stain to a small one and finally back to a large one.
In regards to the self destruct mechanisim of the Nostromo, It is said that the time from the setting to detonation will be 10 minutes. This is also confirmed by the voice of "Mother" who says, right after Ripley initiates the sequence, that the detonation will take place in "T-Minus 10 minutes" However, in the next shot you see one of the monitors which shows a countdown with 10 minutes and an extra 30+ seconds on it.
The menu selection screen on "Mother" has "L. ALLIGNMENT" mis-spelled.
while Parker is decapitating Ash with the fire extinguisher his T-shirt is not torn, just after he says "Ash is a goddam robot" his T-shirt is now torn and held together with a safety pin.
In the scene where Kane is struggling on table shortly before the alien rips through his chest, if you put it in slow motion (it's probably best seen on DVD) just before the first patch of blood appears you will see his t-shirt ride up and you can see something strapped to his chest. This is some sort of pack containing fake blood that discharges on to his t-shirt.
When Ripley is heading towards the Shuttle towards the end, just before she finds Jonesy, there is a POV shot where the camera is walking towards a ladder. If you look at the floor you can see the dolly that the camera moves on.
On the DVD version, following the chest-burster scene as the camera pans around the darkened corridors on the Nostromo just prior to Dallas ejecting Kane's body, what appears to be a boom-mike is visible only for approx two seconds to the left of the screen.
When Ripley goes down to check out how Brett and Parker are doing with the repairs, she says: "Don't worry Parker. (pause) You'll get whatever's coming to you." In the short pause between these two sentences, you can hear Ripley say something like "You have". It seems to be a wrong line which has been deleted, but not properly.
When Ripley is talking to "mother" by typing, it types "Emergency command overide 100375". "Override" should be spelt with two R's.
It can be seen multiple times throughout the film towards the end that there is no cat in the box. This is best seen when the front or back of the box is toward the screen when Ripley is moving down a corridor.
When Ripley is trying to set the detonation of the Nostromo, the sequence begins before she activates the fourth and final fuse on the self-destruct control panel.
In the infirmary scene where Ash, Dallas, and Ripley are looking for the facehugger that has detached itself from Kane, just at the moment when Ripley is looking under the table where Kane is lying, Dallas is empty-handed, he knocks something over and gives Ripley a fright and says sorry while at the same time holding a light in his right hand that was not there a second or two earlier.
When Ash attacks Ripley and Parker beats him off, the android gets up again and tackles Parker. Look closely as Parker crawls up against the wall...the body of Ash isn't a body at all...it's half a mannequin that doesn't even have a lower body connected to it, and it is visible when Parker's legs spread and you can see that there is nothing under Ash's torso except a big hole where the lower half should connect.
When the crew split into two teams of three, Ash gives Ripley a movement sensor, which he tells her detects movement in the direction its pointing. However, when Ripley points the sensor at Brett and Parker (who are both moving at the time) it doesn't detect their movement.
In the scene were Ripley is in the escape pod and has the space suit on, she hits the button to open the door and blow the alien into space. It is most easily viewed in frame by frame mode on DVD, but if you look at the shot were you see the alien getting sucked backwards you can see the wire coming out of its back.
When Parker shoots the blowtorch at Ash, Ash's face begins to melt off. When the skin melts off we see, in slo mo, that the dummy they used has a sealed mouth.
Before Lambert is killed, the alien twists its tendrils around her leg, and we see that she has sneakers on. However, when Ripley notices Lambert's dead body (hanging?) she is barefoot. [An editing, rather than pure continuity mistake, as the rest of the scene was cut. According to the novelization, Lambert was actually intended to be shown completely naked and sexually ravaged. Director Ridley Scott had toyed with the idea of creating the illusion of the Alien having raped her before her death. He thought better of it and cut the scene. Still a mistake, but there's why.]
After the alien leaves Kane's face and the rest of the crew are looking for it in the infirmary, there is one shot that bears re-watching. When Ripley is looking upwards over the prone Kane, you begin to see the dangling tentacles of the alien in the background. At the same time, the collar on her outfit begins to pull downward, un-naturally, until the alien drops onto her shoulder. I believe there was some sort of string or rope fed from below, through her clothing, and was attached to the alien and was pulled to have the creature drop onto her.
When Dallas is in the air vent trying to flush the Alien out of the ship he is carring a flamethrower. Right before his demise, he is told by Lambert to "Get out of there" or something to that effect. In the next shot you see him descending a ladder clearly WITHOUT the flamethrower. However, in the shot after that (when he is lowering himself to the bottom of the ladder, right before the alien gets him) he somehow has the flamethrower again (it even got reslung around his shoulder).
In the scene where the crew is chiding Parker for Brett saying nothing but 'Right' all the time, Brett's cigarette is first short, then long then short again.
When Dallas, Kane and Lambert are exploring the alien spacecraft, you can see that there are wipe marks inside of their helmets that change between shots, most notably on Kane. This is because the helmets were built with out sufficient exhaust systems for the actors. Of course, the characters wouldn't be able to wipe the inside of their helmets with them on.
Disappearing Android Juice - When Ash has gone crazy and is attacking Ripley, his white android juice/sweat/fluid is flowing from his forehead. After he throws Ripley into the room with the nude pictures on the wall there is a new shot. In this new shot Ash is walking into the room but there is no android juice on his forehead.
The amount of Alien slime on Dallas' hand changes between shots.
When Dallas, Lambert and Kane first discover the Space Jockey, the room is so well illuminated you can see the Jockey, its cannon thing and the floor around it perfectly. In all close shots, it's suddenly pitch black and all we can see is the small areas lit by the crew's helmet lamps.
Near the start, when Dallas is at the entrance to Mother, one of the lights to his left, the fifth one down from the ceiling, is not lit. The next shot from inside Mother looking out shows that light is now lit. This exact same thing happens a second time when Ripley is entering mother later in the movie. These two scenes must have been shot at the same time.
In the final sequence aboard the Nostromo, as Ripley is trying to find the buttons that will release steam and open the airlock to drive the Alien out, watch the close-ups of her gloved hand manipulating the controls. Complete, undisguised "trees" of model kit parts are visible as hastily applied detail. You'd never notice in the theatre, but now we have DVD players.
In the scene where Ripley fails to override the self-destruct system she hits the computer with her flamethrower. As this happens it cuts to the screen which displays 10 minutes left until detonation, when really it's under 5.
As Ripley stumbles away from the self-destruct system, The cooling rods are not visible. A few seconds later, in close-up, they can be seen to be above the edge of the compartment they are in.
When Ripley is in Mother, you can almost read the words on her face as if a small projector is beaming these words on her. The screen she is looking at has 4 lines of green text. The image on her face is 1 line of white text.
They use the same shot three times when showing the acid eating throughout the ship. After the try to cut the finger off of the face sucker, acid begins to burnt through the decks. When they have gone down 1 deck and look up the see where the acid came through. This is shown at 0:39:50. They then move down 1 more deck and look up again. The acid is just beginning to burn through. Then they look up again and it is the same shot that was used before. The same hanging acid on the right with the drip on the left. This is at 0:40:20. After the acid has neutralized, they look up at the hole. It is the same shot again at 0:40:57.
In the scene where the crew are dining together just before Kane meets his grisly end, the scene cuts from a long shot, where Parker is saying something, to a closer shot, with the conversation continuing as before. The problem is that Parker's voice can still be heard, but his lips aren't moving.
When the crew are searching for the missing face-hugger in the medical bay, Ripley's shirt can be seen to move to her right just before the face-hugger lands on her - indicating the puppet to be connected to her by a wire.
After Ripley fails to shut off the auto destruct sequence, she runs through a corridor filled with gas. As she exits from the gas right before the shot cuts away we see her pass by a full sized light. Beside this light is the clear arm and head of a lighting crew member. (This is acknowledged on the DVD commentary).
When the dead facehugger falls onto Ripley in the medical room, it lands on the floor with its legs up. The distant shot shows its tail has looped under its body, but the close-up shows the tail entirely straight.
When Ash tries to kill the semi-conscious Ripley by choking her with the rolled-up magazine, she begins to gag before the magazine even touches her lips, even though there is nothing in her mouth or throat yet.
When Tom Skerritt first "interfaces" with Mother after being awoken, he says, "Good morning, Mother" - it is not even close to being Tom Skerritt's voice.
When Ripley is setting the ship's self-destruct mechanism she goes to a panel in the floor. In this panel there are four holes with four screws next to them. When she inserts the first screw she has to manually lift up the cylinder to activate it. It also makes a sound as it is lifted. After she inserts the screw into the second cylinder it cuts to a view in front of her. The cylinder makes the same sound as it raises, but Ripley is not lifting this one. Her arms are doing nothing. When she activates the last cylinder she once again has to lift it up manually by the inserted screw. Based on the design of the mechanism it is apparent that all four cylinders have to be manually lifted, but Ripley does not lift the second cylinder. It lifts itself.
When the engines are fired to kill the alien it drops out of the engine 3 times. This is for cinematic effect but still a mistake.