Factual error: The vents that Hunt and his sidekick crawl down at CIA Headquarters are standard galvanized steel box vents; they are very common in the building trade. Try walking or crawling down one - you'll make a noise like the sky is falling down. People will be able to hear you for miles. Every person in that building would know somebody crawling about in the vent system. (This error applies to dozens of films, not only this one).
Factual error: It is barely credible that a young Victorian woman like Elena would even think about wearing a goatskin miniskirt - exposing her legs in those days would be akin to walking about topless nowadays. Even if she did those bright yellow cotton knickers - gleefully visible in the scene in the beehive - are in no way from the 1860s. Her pants are a hundred years ahead of their time.
Factual error: Near the end of the film, Knox is flying a Huey helicopter, and the Angels hitch a ride by shooting it with a speargun and dangling on the line behind it. Suddenly adding about 200kg to a Huey in flight like that is going to cause all sorts of problems with the trim and airspeed of the aircraft. The pilot would know immediately that something was wrong. (01:23:20)
Factual error: Why is Hilts not wearing a uniform? A serving officer captured behind enemy lines in civilian clothing risked being shot as a spy. If a prisoner's uniform was too worn or damaged to wear, it was routine for the German authorities to replace it - a P.O.W. in civilian clothes is an obvious escape risk. He is wearing a pair of tan chinos, a cut off sloppy Joe sweatshirt, both ridiculously anachronistic - Sixties hipster fashions - and nowhere even close to a World War 2 uniform. He is also wearing Army Type III Service boots - something that would never have been issued to a fighter pilot.
Other mistake: When the stormtroopers break into the control room, the stormtrooper on the right of the screen hits his head on the door frame. On the DVD release they've added a thump when he hits it. (01:18:55)
Visible crew/equipment: When Tom and Sonic pull over and the mini drone explodes, knocking Sonic unconscious, the camera pans away and you can see emergency vehicles blocking the road on the right of the screen, presumably closing down the road for filming. (00:59:55)
Continuity mistake: When Sam is in his bedroom, after he finds the Cube sliver it falls and dramatically burns a hole through the floor into the kitchen. But Sam's bedroom is over the living room (there is nothing on the ground floor below Sam's elevated bathroom, and in the first movie Jazz hides in this open space), and the kitchen is actually located between the den and dining room, at the other end of the house. If they were to follow the actual floor plan of the house, the Cube sliver would have landed in the area of the piano in the living room, but where would the fun have been in that? (00:12:30)
Continuity mistake: Sometimes Shrek's front door opens outwards, at other times inwards, yet it can't be "two-way" because whenever it closes, it slams against the frame. (00:10:55 - 00:13:45)
Audio problem: When Luke says, "Now all we gotta do is find this Yoda, if he even exists," if you look closely, his mouth never moves.
Visible crew/equipment: In the "Battle of Carthage" in the Colosseum, one of the chariots is turned over. Once the dust settles you can see a gas cylinder in the back of the chariot. (01:22:55)
Plot hole: How does the little girl Nina know Ferdinand's name if only the animals can communicate with each other? They're all calling him Ferdinand before she "names" him that.
Continuity mistake: In the final fight scene on the plane between Jinx and Agent Frost, Jinx is slashed across her stomach, drawing blood. In a later scene, when Jinx and 007 are pouring diamonds over one another in the hut on the cliff, her stomach is unblemished. (02:02:25)
Continuity mistake: After chasing down Sully, the yellow Porsche is totally wrecked on the left side, until Arnie drives it away, and it's fine. Later, when Arnie and Cindy arrive at the hotel, the car is wrecked again. (00:39:50)
Visible crew/equipment: When Melissa dodges the truck that has fallen from sky and Dusty rushes to open a door and help Melissa get out of the truck, the reflection of a camera is seen in the bottom right corner of the truck window. As they move out and pan to the right, you can see a reflection of the same camera and cameraman at the bottom right corner of the truck door as they move away. (00:33:50)
Factual error: Trevor - a Professor of Geology - boasts about having an article published in Scientific American, and that is not something any scientist would do. Scientific American is looked upon with slight disdain by the scientific community, considered to be a populist crowd pleaser. It is not even peer reviewed. Considering that he has just turned the geological and archaeological worlds on their heads he would have been better off publishing in Journal of Geological Research or Geology, both prestigious professional journals.
Continuity mistake: In the end, when the President is visited by the X-Men, he receives a blue binder, which is laid in front of him on the table. When they have left, you see a shot including the President's desk, and you can see that the only thing he has on the table are some sheets of paper, stapled in the upper left corner, opened up. Then the shot changes to a close-up of the President, and then back again, and you see the blue binder in front of him, closed, and the papers have disappeared. (02:01:40)
Visible crew/equipment: Just as Jack says, "On deck, you scabrous dogs," to the very left edge of the screen over Jack's shoulder is a grip crew member with a tan cowboy hat, white short sleeve tee shirt and sunglasses, just standing there looking out to sea. (02:12:35)
Revealing mistake: In the swimming pool scene, when David is sitting at the bottom of the pool, you can clearly see a scab on one of his knees. (00:43:00)
Continuity mistake: In the first film, it is mentioned several times that Kevin is 8 years old. However, in this film it is stated that he is 10. When his parents are in the Miami airport security office, they say that he was left alone last Christmas. That would make him 9. Both films take place the same days, from about three days before Christmas until Christmas morning, so even if Kevin is born around Christmas time this is still a mistake.
Continuity mistake: There's an electrical outlet on the wall below the window (aligned with the window shade's loop) in Sid's room near the Megadork poster, but when Sid throws Woody to the floor and raises the shade (before he scorches Woody's forehead with the magnifying glass), that outlet has vanished.
Suggested correction: Knox wasn't a trained pilot. Either he had no clue to what was going on, or he thought something may have been wrong, but didn't know what to do about it.
Taking off and landing a helicopter are by far the most intense and difficult part of a pilot's training. Seriously, 99% of learning to fly is learning how to land and take off. If the pilot is skilled enough to take off in a Huey he is easily skilled enough to notice a massive additional drag on his helicopter due to the additional weight of the angels and the air resistance put up by such a bulky protrusion on his aircraft. If he isn't skilled enough to notice that, he isn't skilled enough to take off in the first place.