Factual error: While the Confederate captain is explaining the mission, a couple of the "patriots" are inserting cartridges into their Colt Peacemakers. A neat trick, since the Civil War ended in 1865, and the Peacemaker wasn't introduced until 1873.
Factual error: When Jimmy Stewart is almost down to the runway during the bad weather, the aircraft exterior shots show the type of cloud tops found only at high altitude, not low to the ground.
Factual error: The opening scene shows Spencer Tracy on a crack streamliner in the desert east of Los Angeles, featuring red and orange coaches. Such equipment was used by the railroad on only two trains, neither of which crossed the desert east of Los Angeles, and both of which had matching red and orange locomotives. In the film the train is pulled by a dark gray locomotive normally used only to haul freight, and in a close-up shot the number in the locomotive is preceded by an X, which in the language of railroading refers to an extra train.
Factual error: Near the beginning of the film, there is a reference to Capt. Merriwether Lewis being summoned to the "White House." That scene takes place in 1804. In reality, the Executive Mansion was not called the White House until 1811.
Factual error: All the troops in the Fetterman massacre are cavalry. In fact, the majority of the detachment, including Fetterman himself, were infantry.