There's a typo in the second paragraph of Beck's dossier. It says "smuggests" instead of "suggests".
It is mentioned twice that Beck has to pick up a blue bag in the gym, but when they try to catch him, his bag is brown.
Emil Beck's dossier has his DOB listed in the Age column.
When the plane is going down and they say they are 100 miles East of Boulder, there is no mountains what so ever there. So when the plane regains control and barely avoids hitting the mountain, the only thing they would hit is a flat area of ground in the plains.
Riley says the glitch is affecting "both" engines. The plane has four engines, not two.