(at around 1h 26 mins) At the end of the movie when the four predators carry the body of Scar (Main predator) into the predator mother ship. You can clearly see the four predators struggling to get up the ramp. In the movie's theatrical release commentary Paul W.S. Anderson revealed the predator suits were "too heavy" and that the ramp was slippery due to a substance being added to the ramp to make it look more shiny.
(at around 38 mins) Sebastian sets the clock on the sarcophagus to October 10, 2004 - 10/10/2004, because the Aztec calendar was supposedly based on 10's (the decimal system, erroneously called "metric" here). Yet, why would an Aztec civilization set a calendar to align with the Gregorian calendar, which is what our modern calendar is and wasn't developed until centuries later by the Romans? The Aztecs would not recognize what we call "October" as the 10th month.
In the movie the whaling station was abandoned in October 1904, when in fact it wasn't until the following month that the first whaling station, Grytviken (Cauldron Bay), was established in the Antarctic, and not at Bouvetøya, but in South Georgia. Modern whalers didn't reach Bouvet until the 1928-29 season, and these were operating with factory ships offshore. In 1928, the UK waived its claim on the island in favor of Norway, which had occupied the island the previous year. In 1971, Norway designated Bouvet Island and the adjacent territorial waters a nature reserve. Since 1977, it has run an automated meteorological station on the island.
(at around 11 mins) Graeme Miller's description of the aurorae as being caused by protons and electrons in the atmosphere is inaccurate. Aurorae are caused by the interaction of high energy particles (usually electrons) with neutral atoms (oxygen, nitrogen...) in Earth's upper atmosphere. However, as a chemical engineer, his knowledge of atmospheric photochemistry may be expected to be somewhat rusty.
(at around 48 mins) Sebastian erroneously says that the Aztec calendar was metric (he means based on 10, which is not "metric", but "decimal"). In fact, the Aztecs had two calenders and neither was decimal. One was vigesimal (based on 20) with twenty days in 13 "months." The other was a 365-day year count.
(at around 37 mins) Sebastian refers to "the Long Count" while describing a calendar that he refers to as "Aztec". The Long Count was a feature of the Mayan calendar system; the Aztec calendar, although based on the Mayan, didn't use the Long Count.
Most of the weapons used by Weyland's team feature laser sights. Anyone with any kind of tactical sense or common sense would know that bumbling around with a bright green laser sight activated while being hunted by giant, stealthy monsters would be incredibly stupid. The laser beam leads right back to the shooter's precise location.
(at around 2 mins) When Alexa is climbing the Lho La ice fall in Nepal, you can see a overview of the edge where is climbing to. There is nowhere a helicopter too be seen, yet after 30 seconds (duration of the phone call) the helicopter manages to land, turn off the engine (spinning down rotors takes much more than 30 seconds), and let Maxwell Stafford out of the helicopter and walk towards the edge to meet Alexa, all without her hearing or noticing a thing.
As the Predator ship passes by the Moon on its way to Earth, we can see the far side of the moon lit up, so from Earth it should be a new moon or at least a crescent. Yet, minutes later, it's a full moon.
(at around 54 mins) The Predator cuts off the tip of the Alien's tail, spewing green acidic blood, and then tosses him through a column and into another room. As the Alien flies in slow motion, you can see that there is no blood on his stump, but immediately after, it's covered again.
(at around 1h 10 mins) When Lex catches the alien on the spear, it swings its tail at her and punctures the wall. Then the camera cuts back to the alien for a split second, then back to Lex as the alien attempts to hit her on the other side. You can clearly see that there's not a scratch on the wall that was just punctured.
In the unrated edition of the film, a satellite focuses in on Bouvet Island, but in that scene, the island is erroneously situated in the approximate location of Peter I Island, which is quite a distance from the actual location of Bouvet Island.
The island is referred to as "Bouvetoya Island" (the English name is Bouvet Island, "Bouvetøya" is Norwegian for Bouvet Island) but the real Bouvetøya is much further north and east than the satellite images suggested.
(at around 16 mins) Lex says that the pyramid would be directly underneath the whaling station, but the hole made by the predators is at an angle that would put the pyramid almost 3/4 of a mile away from the whaling station.
The film justifies the existence of a pyramid in Antarctica by saying that the continent once had a warmer climate with a lush ecosystem. This is true, but that was millions of years ago, not during human history.
In the movie, nearly complete whale skeletons are shown around the whaling station, when in fact carcasses were normally towed offshore by the whalers, and the only bones that would have been seen were a few rib or jaw bones that had washed ashore near the flensing plan of the station, not within the station complex itself.
(at around 2 mins) When Alexa Woods is climbing the Lho La ice fall in Nepal, she's about 10 body-lengths from the top edge. From the moment she answers the phone she reaches the top in about six steps. You can't take steps longer then your body.
(at around 12 mins) During the space-shot of the predator ship shooting a beam to "drill" a hole to the pyramid, we see a beautiful shot of the Earth from space. However, we can clearly see both the day-lit side and the night-side. In reality, if we were looking at the Earth from space, we would only see the lit side while the night side would be completely dark (for example, look at any picture of the Earth as seen from the moon).
(at around 29 mins) When the expedition first reaches the hidden pyramid, one of the characters examines the wall markings after rubbing away the cobwebs from the stone. Are there any spiders that thrive 2000 feet below sea level in Antarctica? Spiders and other arachnids have been known to survive in extremely hostile environments, including at high altitudes, in climates of intense cold and where food supply appears to be scarce. The climate inside the pyramid was warm enough that the humans' breath did not condense. Other survival factors may have been present. Also, the material may have not been spider webs, but strings of dust and particles accumulated over time.
(at around 48 mins) It's claimed that the pyramid will move every ten minutes because the Aztec calendar is based on the "metric system". Time measurement has nothing to do with the meter. What he means is the decimal system. Modern measurement of time (24 hours in a day) is not decimal. Thus, each Aztec hour should be around 2.4 hours (1/10 of the day). As such, it would be more probable that the pyramid would move every 14.4 minutes.
The time-frame for the Alien life-cycle(facehugger->chestburster->warrior) is made to seem like mere minutes in accordance with Sebastian's time-theory(10 minutes). From the other Alien movies, the same life-cycle can take hours or even days to complete.
The legs of the practical and computer-generated Aliens don't correspond. The practical ones have human-like joints and feet, while the CG versions have an extra joint at the ankle and much longer toes.
The goof items below may give away important plot points.
(at around 1h 17 mins) When Alexa and the Predator 'Scar' find Sebastian all the eggs are open and presumably empty, but when we see from the Predator's view the eggs are all closed and facehuggers are preparing to emerge.
(at around 1h 19 mins) When Alexa and Scar are on the sled trying to get away from the bomb, Alexa is holding on tight with both hands. When she jumps off the sled and runs, she has the head shield on her arm, covering her hand. She wouldn't have had time to pick it up once the sled stopped.
The film gives confusing and inconsistent accounts of geography of the island and the pyramid. The pyramid is supposedly under 2,000 feet of ice, yet the tunnel leading down to it begins at the (sea level) whaling station. The geographical survey (as well as the obvious in-story shots) show that the ice tunnel slopes gently down towards the pyramid entrance, therefore not on top at all. The whaling station is thus supposedly built on ice instead of rock; this is a ludicrous proposition as it would only be constructed in a region where ice melted enough each summer to allow whaling ships to dock. Anything built on ice that thaws significantly each year would not last 100 years. This arrangement also places the pyramid and a large amount of ice below sea-level; the buoyancy and natural flow of the ice pack makes this highly unlikely and is not something that could be accurately described as an island in the first place. The top of the tunnel is at the whaling station and descends at a "perfect 30 degree angle" to the pyramid (thus placing it over half a mile away horizontally, you'd travel 3464 feet horizontally), yet we are told satellite imagery shows that it is directly beneath the whaling station. Further confusion is caused by the scene at the end of the film in which a large tank falls into the water and plunges hundreds of feet towards an unseen ocean floor, supposedly directly offshore.
At the end of the movie, Scar is speared through the chest with the tail of the mother alien. As Scar has already been impregnated with an alien embryo, this wound would have killed the alien in his chest, but it hatches at the end of the movie. It was also established in Alien³ that the aliens take special care to avoid harming their embryos' hosts.
(at around 1h 3 mins) When Miller gets cocooned and kills the first face hugger, he fires six shots from Verheiden's Desert Eagle. After Miller realizes he's in trouble and the shot pulls back into the hall, he fires six more times before he screams. The maximum magazine capacity for the Desert Eagle is nine shots for the .357 Magnum.
(at around 1h 19 mins) When the Predator and Alexa turn around after the whaling station falls into the ground, the shot of them is reversed (notable by the marking and pressure tubes on the predators helmet). When Alexa and the Predator are running from the explosion - across the whaling station - her "shield" changes hands.