After waking Scully up, Dr. Carpenter then goes on to explain the basics of genes and base pairs. As a medical doctor, Scully would already know about this, as it's basic high school biology.
When Scully attempts to gain entrance to the holding facility where the alien body is being kept, she hears a security guard ask her for the "Project Password" through a speaker grate. If you look closely, embossed on the bottom of the grate it says, "Cold Water Only". Apparently this grate was appropriated from another source and wasn't a speaker grate at all.
The police chase involves a Buick Century as the suspect's car. However, when Mulder asks the alleged owner (Dr. Berube) about his car, they mention that it is a Ciera (Oldsmobile), a different car altogether, though it was built on the same platform. What's more, the Buick that is shown is clearly from the late eighties (1988 at the latest) judging from the headlight style. Scully and Mulder determine that one of the two identical cars belong to a rental agency and it is extremely unlikely that a 6-year old (or more) car would have been kept in a rental agency's fleet.
In the picture of the suspect's car captured from the video, the license plate is clearly visible prior to Mulder having it "enhanced", after seeing the replacement car in police custody. Mulder even comments that the plate "isn't visible" even though it's been clearly shown on the screen moments prior.
In the early part of the police chase, we see the suspect's car crossing a railroad track; a CN (Canadian National) logo is clearly visible on the approaching locomotive. The chase supposedly takes place in Maryland and the CN's network, even in its American network, does not go close to Maryland.
Dr Berube allowing two strangers (Mulder and Scully) into an animal research facility without protective gear (to minimize the risk of human-borne pathogens) is a major safety violation. However, the research company is later revealed to be involved in shady dealings, so this could be a deliberate character error on the producer's part.