- The action starts aboard the Predator ship that collected Scar's body from Bouvet Island, as seen in Alien vs. Predator. However, the Scout Ship shown does not match the Mother Ship seen leaving Earth at the end of the previous film; aside from the obvious design differences, the ship in Aliens vs. Predator: Requiem is a much, much smaller vessel than the one seen in Alien vs. Predator. This mistake was corrected in the Unrated Edition.
- Several things surrounding the birth of the Predalien in this movie are noticeably different to what was seen in Alien vs. Predator. The lights on the table are different. The Predalien itself bursts out of Scar differently compared to the first film, while its inner jaw, seen in Alien vs. Predator, has been removed.
- When the Scout Ship crashes, it passes directly over Buddy and Sam Benson, then strikes the top of a hill, then finally comes down in the forest on the far side of the rise. The scale of the trees in this sequence show that the vessel travels a significant distance (at least several miles) during the crash, but despite this, Buddy and Sam are able to run to the wreck in a matter of minutes.
- Jesse lives at house number 1472. Yet when Ricky delivers the pizza, the sign on the light post outside says 1012.
- Mark makes fun of Ricky's pizza shop uniform, saying that he thought Halloween was in October. However, given that Alien vs. Predator took place on October 10th, it is October.
- The blood that splatters on the swimming pool window when Dale's friend is killed by the Xenomorph disappears in the next shot of Ricky jumping down off of the dumpster.
- Wolf pours some of his Dissolving Liquid into the pool to destroy the bodies of Scotty and the Warrior that killed him, and when Ricky and Morales arrive later, we see that it also causes all of the water to boil away. However, it does no damage whatsoever to the pool itself. Given the portrayed potency of the liquid, it seems unlikely that it would be able to do the former without also doing the latter.
- Again, Alien vs. Predator tells us this film takes place soon after October 10th 2004, yet in the maternity ward of the hospital, two separate monitors give the dates June 3rd 2006 and September 23rd 2005.
- When the survivors enter the gun store, Morales walks into building and Dallas steps into the doorway behind him. When the camera cuts to show Morales checking out the interior, the doorway is suddenly clear and Dallas does not appear until Morales beckons him to follow.
- Kelly stops the Stryker when she realises Colonel Stevens may be lying about the helicopter evacuation in the center of town. However, when Morales and several other survivors elect to continue to the supposed pickup location, they head off in completely the opposite direction to the way the Stryker is facing; if it was previously heading for the evacuation point before Kelly stopped, they should be driving in the same direction as the Stryker.
- In the scene where Morales leaves the group of survivors in the Stryker, the slide on Jesse's gun is visibly locked back, meaning it is out of ammo, despite the fact she has yet to fire a single shot.
- Ricky is stabbed in the shoulder by the Predalien in the hospital, but the wound later disappears. He also uses his arm several times in a manner that would be totally impossible given such a severe wound.
- After Dallas shoots the gate with his Plasma Pistol at the end of the film, the wire fence keeps changing shape in different shots.
- Near the end of the film, Kelly kills a Xenomorph by shooting through the helicopter's front window, yet its corrosive blood, which can be seen splashing liberally, does no damage at all to the aircraft. Later, when the helicopter is in flight and trying to escape the nuclear blast, even the bullet holes in its windshield are gone.
- The final act of the film takes place amidst a torrential downpour, yet when the survivors are found by the special forces team at the helicopter crash site the ground and trees around them are completely dry. Even with the sun shining, there's no way the environment could completely dry so quickly.
- The alterations made to the beginning of the film in the Unrated Edition to correct the goof concerning the Predator spacecraft's appearance create an additional plot hole — specifically, it makes no sense that the Predator Mother Ship would leave Earth, the hunt in Antarctica complete, only to have the Scout Ship later detach and return to the planet for no apparent reason.
- When Wolf kills Ray, he skins him and hangs his corpse from a tree. However, Wolf is supposed to be on an urgent mission to stop the Xenomorph infestation as quickly as possible before it can spread. It therefore makes no sense for him to waste time mutilating people who are of no importance to this mission.
- The Greyhound bus is seen arriving in Gunnison at the beginning of the film, with the destination sign in the front window marked "CRESTED BUTTE". Although Crested Butte is 28 miles north of Gunnison on CO-135, there is no Greyhound transportation of any kind to Crested Butte. Additionally, Greyhound offers no services on their fleet of buses to Gunnison itself, as these are contracted out to another bus company, Black Hills Stage Lines, Inc.
- The crashing Predator ship would almost certainly have been seen or heard by the people of Gunnison. As an example, the meteor that entered the Earth's atmosphere over Chelyabinsk, Russia in 2013 was only around 20 meters in diameter, yet was visible from as much as 100 km away. In the film, only Buddy and Sam seem to notice the much larger crashing ship.
- The climate, and hence the vegetation, of the Gunnison area is quite unlike that seen in the film. The annual precipitation of Gunnison is less than 11 inches and does not support the growth of ferns or any other lush vegetation. Much of the movie was in fact shot in the temperate rainforests of British Columbia, hence the difference.
- The uniform Kelly is wearing when she returns home features the United States Marine Corps' digital desert camouflage pattern, but the jacket has "US ARMY" chest tags (which are also the wrong size and in the wrong position). The United States flag and unit insignia are also on the wrong arms.
- AN/PVS-7 night vision goggles are a very expensive piece of equipment, and the US Army would not allow a soldier to take them home so that their children can play with them, as Kelly does in the film.
- Although some scenes of the film take place in the sewer system underneath Gunnison, no such system exists. The Gunnison sewer system is limited to piping and does not include underground catwalks.
- Morales does not notice Ray's skinned body hanging from the fir trees until he is standing directly under it, yet it is clearly hanging well below the forest canopy, and with no branches to obscure it, it would have been plainly visible from much further away.
- There are no nuclear power plants in Colorado, and no power plants of any kind in Gunnison.
- The National Guard is called from Colorado Springs and they arrive shortly; Colorado Springs is three hours away from Gunnison.
- National Guard soldiers are depicted wearing Army Combat Uniform (ACU) battledress. However, ACU was not issued until 2006, two years after the film is supposedly set. The National Guardsmen are also armed with fully-automatic M4A1 Carbines, which in reality would only be issued to special forces personnel. National Guard troops would instead carry the similar M4 Carbine, which is limited to either semi-automatic or three-round burst fire.
- The National Guard armored vehicle used by the survivors is identified as a Stryker, but it is actually an Omni International V-150-S prototype. The V-150-S has never been used by any branch of the United States military. The V-150-S was used because the production could not secure the use of a real Stryker from the US military.
- Given that Gunnison covers only 3 square miles, Colonel Stevens' map is showing a "pressure damage" radius of barely 1/4 mile. In reality, a 200 kiloton nuclear explosion would level all structures within at least one mile. The "heat damage" radius on Stevens' screen is even more understated.
- The bomb dropped in the movie is incorrectly displayed as a "MK 83" on the screen showing the purported damage assessment of the tactical nuclear weapon. In actuality, the Mark 83 is not a nuclear weapon at all; it is a conventional weapon with a modest amount of high explosive inside. It would not be capable of the damage estimated on the readout. There is, however, a nuclear weapon employed by the US military designated the B83, which corresponds to the weapon we see in the film.
- When Ricky is firing his Glock from the helicopter before it leaves the hospital, he runs out of ammo and the slide locks back. The sound of a hammer repeatedly falling on an empty chamber can be heard as he continues to pull the trigger, yet a Glock (like all semi-automatic pistols with a reciprocating slide) does not make any noise if the trigger is pulled once the slide has locked back.
- The nuclear device used at the climax of the film is shown to be launched by a Lockheed Martin F-22 Raptor. However, the designation used on the tactical display the General is looking at is for a much larger weapon that cannot be deployed by a fighter/bomber.
- The Raptor is travelling at supersonic speeds when it drops its payload, yet the bomb falls straight down when released. In reality, the plane's inertia would make it travel forwards, at least initially. It also deploys retarding fins moments before it detonates whereas such fins would deploy as soon as the weapon is released. Moreover, the B83 does not use solid retarding fins to slow its descent, but rather a fabric parachute.
- When the helicopter is hit by the blast wave from the nuclear explosion, internal shots show its horizon indicator is spinning. This would only be possible if the helicopter was flying barrel rolls, which it clearly is not.
- When Wolf is searching the sewers, his Whip and Wristblades suddenly switch from his right side to his left, revealing the shot has been flipped horizontally.
- The helicopter that the survivors flee in has a Canadian registration number under the front doors, beginning with the letter "C" (the movie was filmed in Canada). Any aircraft that operates exclusively inside the United States, as would be the case with a helicopter based in Colorado, would legally require a US registration number.