(at around 28 mins) Michelle was involved in a car accident, which left her bruised at several places on her face. In the scenes following Col. Belt's press interview, there is absolutely no hint of any scar or injury on her face.
Before the car crash, both cars have their wipers on because it is raining hard. And it is foggy. This poor visibility contributes to the car crash. After the crash it is not raining and not foggy,
(at around 22 mins) Launch pad personnel in orange suits are seen at the base of the main Shuttle engines less than two minutes before launch. In reality, all close-out crew depart the launch pad three hours prior to launch.
Throughout the episode NASA addresses the shuttle crew as "OTC" while in reality OTC stands for Orbiter Test Conductors. The OTC is the individual in charge of the engineers monitoring the hardware and software on board the orbiter itself. Other test conductors are responsible for the external tank and solid rocket boosters, the payloads, support operations, landing operations, safety, communications and other functions.
A flight of Navy Blue Angels flies over the funeral. The colonel being buried and most of the service members present were Air Force personnel.
When looking for the evidence of Colonel Belt's knowledge of the sabotage, Scully is going through a series of numbered dossiers, two of them bearing the same number 54.
Mulder states he is a big fan of Col. Belt and watched his Gemini 8 mission when he was 14 years old. Gemini 8 flew in March 1966. It was later established in the series that Mulder was born in October 1961.
Since the first televised US space mission was Apollo 7, in October, 1968, Mulder could not have stayed up to watch a Gemini EV event.