When Scully is asleep in the car and a UFO (presumably) flies overhead, the glass shatters in the back. However, later, when Mulder and Scully are being detained by the "National Security" guys, the back windshield is shown intact.
When Mulder escapes the motel bathroom and drives away, the car suddenly has no rear spoiler, which it had in the scenes before.
In the beginning when SWAT enters the house. The leader of the group has his finger on the guns trigger. A trained police/military would know not to have the finger on the trigger for safety reasons.
The Air Force Office of Special Investigations (AFOSI) should be the lead agency involved, not the FBI.
As Mulder and Scully are driving towards the road block set up by the men in black, Mulder brakes sharply, and the exterior shot through the windscreen clearly shows the stunt doubles in the car.
Towards the beginning of the show, when Mulder is using the restroom in the bar, he is approached by Deep Throat. Mulder notices that the door is bolted shut, even sees that someone is trying to get into the restroom. But when Deep Throat turns around to leave, the door does not show a bolt, nor is it secured by any type of locking mechanism.
When Mulder and Scully are confronted on the road by two cars full of government/military personnel. The guys in suits force Mulder and Scully out of their car and disarm them. One of the government agents takes Scully's pistol from her and removes the magazine. Slots in the magazine show how many bullets are in it, and it is clear that Scully only had one bullet in her gun.
When the airfield security agent breaks the car side window with a fire extinguisher you can see its clearly a soft squishy prop.
When Mulder and Scully are being searched by the other agents at their car the agent who searches Scully takes her gun and pulls out its magazine. He holds the magazine up for a moment and you can see the sides of the magazine are open and shows only one bullet at the top of the mag but only the spring for the rest. This means the gun at most only had 2 bullets (agent did not clear the chamber - another revealing mistake). Useless in case it's needed.
When base security drives up to Mulder on the airfield, he tries to out run them along the length of the airstrip instead of quickly running for the tall grass on the side where he had just came out of.
When narrating her field report at the end, Scully says that she "can cooperate Mulder's account" of the UFOs at the base. She means "corroborate", not "cooperate". A later shot of her computer screen shows that she typed "corroborate" correctly.
The "MPs", presumably USAF, are wearing Navy/USMC officer rank insignia. USAF/US Army insignia are larger and have a different configuration.