Deliberate mistake: Gandu Three Echo, the clone who hits the screen showing the first lottery winner in the movie, complains that he has been around for 7 years and never won the lottery. However, McCord explains later in the movie that the last name tells how old the clones are. Lincoln Six Echo is 3 years old because he is in the Echo generation, and the Delta generation (Jordan Two Delta) is 4 years old. Going backwards, this would make Charlies 5 years old, Bravos 6 years old, and Alphas 7 years old. Gandu Three Echo should have really been Gandu Three Alpha.
Factual error: When the first train wheel hits the ground in the close up, you can see that it isn't made of steel as it deforms as if it were foam. And there is also no damage to the concrete road whatsoever, since the wheels are made of steel there should have been quite a big hole.
Continuity mistake: When they are driving behind the truck, a flat piece of metal falls off. Shortly before it hits the car it is "flying" horizontal (20°) however in the next shot, when it hits the car it is suddenly vertical (90°). No time between the two shots for that immense change.
Continuity mistake: Towards the beginning of the film, when Lincoln and Jordan first escape, we see them running and hiding in the room full of new 'products'. Water is constantly falling from the ceiling like rain, and both of them are soaked, to the point of water running from their hair and clothing in streams. In the next shot, however, when they have just left the room, they are little more than damp.
Continuity mistake: Two members of Laurent's team are in the elevator going up to the 70th floor of a rather tall Gas Company Tower in LA (the building with the giant "R" logo; presumably the building's height has been raised) to go after Lincoln and Jordan. When they step out of the elevator, the display inside says "70," but the floor number outside the elevator says "L," indicating that they're actually on the lobby floor.