In the exhumation scene at the cemetery, the digger driver is seen climbing down from his vehicle as Mulder and Scully pull up in their car. In the next shot you can clearly see the driver getting out of the digger again as Mulder and Scully are greeted by the police/authorities.
When Scully is in her room after the autopsy, the x-ray is attached to her lamp. When first shown, the letters LD are seen on it, yet when the shot changes back to the x-ray after Mulder has left, only an I is visible. Presumably the other x-ray is now overlapping it.
The first time Scully walks into Mulder's office, his "I want to Believe" poster is in full view. Later on in the scene, there are papers stacked in front of it.
During the part where the car's radio and clock go crazy, the sunlight changes. From one angle we see Mulder, and the shadow on his face shows the sun angling in from his left. But the next shot of Scully shows the sun angling in from her right. The shot changes and once more the sun is on Mulder's left.
When Scully goes to Mulder's room, thinking she has the marks, after he has checked her, Scully's hair is behind her collar, but when the shot changes to her going to sit down, her hair is now hanging out.
The footage of their airplane flying is stock footage of the Boeing 727 test plane, which, obviously, would not be carrying passengers on a transcontinental trip. This is a common mistake in many TV shows and movies. Usually the type of aircraft changes between shots.
After their first visit to the woods and back at the motel, Scully is in her room in a robe typing notes into her laptop. When the general building power goes out, her laptop & screen go instantly dark too. Scully says "Great." But laptops run off their internal batteries, not the A/C power. Loss of A/C power would only stop the laptop from continuing to recharge its internal batteries -- if it happened to be plugged into a wall-socket. Scully should have been able to continue using the laptop, but they want her to be interrupted for the next scenes to progress.
The mysterious organic substance found in the tissue surrounding the markings on the victims that Mulder shows Scully on a slide is nothing more than the generic peptide backbone of every single protein on earth. As the Rs represent any possible amino acid side chain, there's absolutely nothing special about the molecule represented or anything surprising about it being found in any sample of human tissue.
When Theresa asks Mulder and Scully for protection, her nose gushes blood. The flesh colored tube that is running down her forehead and from the bridge of her nose to pump the blood is visible.
The monitor of Scully's laptop (seeing when she is entering info about Soames's autopsy) is CRT (cathode ray tube). CRT monitors are only found on desktop computers and not laptops.
When Mulder informs Scully that they lost nine minutes of time, Scully says it's impossible because time is a universal invariant. Since Scully did physics at university, she should know that only the speed of light, and charge are universal invariants.