The interior of the spaceship is obviously bigger than its exterior would account for.
In the first car chase, the agents' car sustains side damage from attempting to force the astronauts' pickup truck off the road. However, when the car turns onto the bridge it is seen to have gained severe damage to the front bumper and bonnet/hood. As it crashes through the side of the bridge its front is again undamaged.
Wide shots of the search and rescue helicopters taking off show the pilots wearing dark-colored flight helmets. In the close-up scenes, the pilots are wearing their garrison caps.
The UFO was damaged by a collision with the launching satellite to the point that it crash landed and killed the occupants. However when the government dropped an airplane loaded with high grade explosives on top of the craft, it wasn't even damaged.
Toward the end of the film, Lew and Steve (the heroes) are driving a gasoline truck, being chased by two government agents. Lew takes a signal flare and goes to the rear of the truck, dumping a large gasoline slick, shutting off the gas flow, then lighting the flare and throwing it on the slick, causing a fire that kills the two agents. The problem is, Lew throws the flare about three seconds after shutting off the gas. The truck is traveling at least fifty miles an hour... meaning that it would have put at least 200 feet between itself and the slick. Lew would have to throw the signal flare 70 yards, with perfect accuracy, for this trick to work. His throw clearly wouldn't carry the flare more than ten or twenty feet.
It is difficult to believe that a linguist, however skillful, could give a detailed, one-to-one translation of an alien language, programming a computer to give instant interpretations, all in the space of a few days.
During the landing of the Shuttle, an announcer reads off the airspeed as "100....90" as the wheels touch down. The actual landing speed of the Shuttle was near 200 knots.
Sheriff Barlow has a revolver in his holster, but the ammo case on his belt is for magazines for an automatic pistol.
When the shuttle deorbits it fires the three main engines. There are powered from the external tank during launch and have no fuel available once the tank is discarded. Instead the shuttle used the smaller Orbital Maneuvering System (OMS) engines for the deorbit burn.
The space shuttle orbiter, while in space, has the standard nose of the NASA's orbiters that went to space, but the landing footage shows a needle sticking out from the tip of the nose. This needle was present only on the Enterprise orbiter, which never went to space, revealing that the landing footage is NASA atmospheric test footage.
Camera shadows can be seen on the car hoods during the chase scenes. In one instance, one can clearly see the camera operator's shadow.
The coordinates shown (N45° W165.4°) is nowhere near Arizona. It's in the north Pacific.
To cover up the UFO landing, Cain and Lafferty decide to discredit Steve and Lew publicly, then just "keep an eye on them." They do not take Steve and Lew into custody, sequester them, or put any kind of pressure on them not to make waves, even after Steve and Lew indirectly cause the deaths of two government agents. This seems to be the worst possible way to cover up a story, as it all but guarantees the two heroes will make trouble.
Reporting on the autopsy, Dr. Michaels states that humans have "an appendix, a tailbone, and a Harderian Gland". The Harderian Gland is only found in the ocular orbits of vertebrates that possess a nictitating membrane, which humans do not have.
A scientist refers to a chemical found on the alien craft as "an element similar to potassium cyanide". Potassium cyanide is a compound, not an element, and no element could be classified as similar to it.