Revealing mistake: When Yoda knocks Darth Sidious backwards over his chair, you can see the stuntman's hand. Sidious's hands are old and his nails are dark around the cuticles, but the hand during the flip is perfectly healthy and a different size. (01:45:35)
Revealing mistake: When the Hudson Ferry captain casts off the large label that reads "Hudson Ferry" is on his left side of his jacket. However, in the exterior shot as he looks out the window at the whirlpool, the label is on his right side. This shot was flipped, and amusingly, the CGI guys actually retouched the words "Hudson Ferry" so it wouldn't read backwards. (01:02:25)
Revealing mistake: When Kadaj kneels in front of Rufus Shinra, watch his sword. As he kneels, it goes through the floor.
Revealing mistake: Aeon's neck freckle swaps sides in one shot, revealing a flipped shot.
Revealing mistake: When Will flies back in through the window and picks up Royal Pain, you can see that the back of Will's jacket is sticking up, which was where the harness was lifting him up. (01:24:05)
Revealing mistake: On Miranda there is a shuttle crashed into the side of a building, but there are no burn marks or a trail from where it had crash landed. The shuttle couldn't possibly have crashed into the building horizontally without crashing diagonally/vertically first, landing horizontally and then sliding into the building. Joss Whedon even states in the director's commentary that some burn marks would have been nice but it only occurred to him about 14 months after it was filmed. (01:17:15)
Revealing mistake: When the talons and E.D.I. attack the fort during their first mission, the explosions show the use of pyrotechnics when A.T.S. missiles explode in a simple blast.
Revealing mistake: At the beginning of the movie, when the guy is bitten in the wrist, if you watch and listen closely when he shoots himself, the blood comes out of his head before he actually shoots.
Revealing mistake: When the president is thrown out of the window by Carpathia, it is obviously just a CG shot. Not only is the president obviously CG, but the glass from the window breaks into neat little triangles. Right.
Revealing mistake: When Ryer and Rand jump off Rand's window and down to the street, they land on a tree. Notice the severed branches; instead of being broken [presumably from the falling bodies], they are cut rather smoothly.
Revealing mistake: In the very first scene, which takes place in a Moroccan sheepherder's meadow, the camera makes some gentle panning motion. The mountains in the distance can be seen noticeably moving not quite in sync with the foreground. The foreground is actually in Texas (according to the director's commentary), and the mountains were added in post production.
Revealing mistake: During the car chase with the railway train wheels, when some of the cars get destroyed and flipped, you can see flame and smoke from the bottoms of the flipped cars where the cannons fired to flip them.
Revealing mistake: When Victor Von Doom is shown proposing to Sue Storm in the space station, for a short moment you can see a reflection of the blue screens they used to create "space".
Revealing mistake: When Charlie is climbing the wall you can see a handhold screwed into the wall when she lets go with her right hand. (00:59:45)
Revealing mistake: In the first person shooter sequence, when Reaper gets the chainsaw, there are many parts where he is moving it around near Pinky, now the beast thing, and it does not have a shadow, and at other times when it is at the same angle, it does.
Revealing mistake: When Walter, Danny and the astronaut are in the kitchen breaking stuff to burn, the smaller boy tries to smash an old style broom on the table. He tries three times, on his final try the shank breaks in half, revealing where it had been sawn nearly all the way through in nice clean line, with only a splintery piece showing where it really snapped.