Revealing mistake: When Non tries to fly at the end of the film, but falls into the bottom of the Fortress of Solitude, watch closely. He appears to hit some sort of safety pad after he falls, making the fog around him disperse very briefly, which shows him safely land on the pad. The fog quickly comes back and covers him as he ducks his head down.
Continuity mistake: When they are in east Houston, Idaho, the helicopter gets knocked out of the air and lands upside down onto a jeep. You see the pilot get smashed into the seat of the jeep real hard and yet seconds later he walks away unharmed.