Deliberate mistake: When Morpheus is facing the twins' car, the road's not all that wide, and there are concrete barriers both sides of him. After he rolls to the side and slices their car, we see a side shot, quite far back from the road, and the barrier closest to the camera has disappeared (presumably so we get a better view). In a closer view, both barriers are back again. (01:29:25)
Deliberate mistake: Almost trivia, but not quite. When Mystique's looking through the guard files to find a suitable candidate, lots of photos flash up very quickly before she finds the guy she uses. Of note is that Bryan Singer pops up in guard uniform (with his own name), and so does someone called "Donner, L". This is most likely referring to Lauren Shuler Donner, one of the producers, and sex is specified as "F", but the photo is of a stubble-coated man. (00:23:10)
Deliberate mistake: In the scene with the first demonstration of the digging laser, they dig/blast quite a hole in the mountain. Even assuming the laser can very easily shatter the rocks substance, still the debris would have to go somewhere, yet there appears to be none. And the amount of power needed to convert matter into energy is not practical.
Deliberate mistake: After the game has entered the real world, and Floop and Minion are there to "save the day", Carmen and Juni throws seven pairs of glasses to them. But afterwords, we see there are only four pairs of glasses on Minion and one pair on Floop, which totals five. (01:11:10)
Deliberate mistake: After Mina leaves the car in Venice, Sawyer just manages to avoid several obstacles on the way, including a bend in the canal. But in the first scene, where Sawyer swerves the car around, its front should have slipped into the water anyway, considering the speed of the car and the tightness of the street, which makes a sharp L-turn at such close quarters next to impossible. But then the scene jump-cuts, and the car is well past the hazard.
Deliberate mistake: When Hulk meets his father at the lab, each one's eyes have a special light on them. This adds for dramatic effect, but it's absurd because there is no direct source of light since each one is in front of the other and their faces are in shade in the rest of the shots.