When Captain Whitfield first gets into the F-117 and the ground crewman hands him his virtual reality helmet, he's not wearing gloves. As he puts on the helmet, he has gloves on.
The bathroom air vent in which Captain Winfield hides from the terrorists does not exist on the C-5.
The aerial refueling boom through which the hijackers "slide" into the C-5 are in actuality less than 12" in diameter and when connected are connected to a fuel line, not a huge dry bay area as shown.
The F-117A was never designed for dog fighting and carried no Sidewinder Infra-red seeking missiles (typically used in a dog fight). Instead it would have carried AGM-65 Mavericks or AARAM's.
(at around 12 mins) The co-pilot addresses the major as "Sir" instead of "ma'am".