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 is a universal invariant.
When Mulder and Scully return to the cemetery to find the empty graves they begin to work out what's been going on and Scully says, "And the force summoned Theresa Nemman's body into the woods tonight." But it was Peggy O'Dell who was summoned that night and was killed running across the highway. Theresa Nemman phoned Mulder to tell him Peggy had been killed and approached the agents for protection at the scene of the hotel fire. She describes her previous experiences of having been summoned to the woods but she wasn't summoned that night. She is summoned the next night.
When Scully goes to Mulder's room, thinking she has the marks, after he has checked her we see Scully's hair is behind her collar, but when the shot changes to her going to sit down, her hair is now hanging out.
When Scully is in her room after the autopsy, we see the x-ray attached to her lamp. When we first see it, we can see the letters LD on it, yet when the shot changes back to the x-ray after Mulder has gone, we can only see I, presumably the other x-ray is now overlapping it.
When we first see Scully, going into the office at the beginning of the episode, we see when she is on her way to the office and when she enters it she is wearing her badge, yet when the shot changes, it is no longer on her, then when she comes out she is wearing it again.
When Mulder and Scully are driving after their plane lands, we see at one point that Mulder has his left hand on the wheel and he is eating a sunflower seed with his right, yet when the shot changes he's driving with his right hand and eating with his left.
During the part when Mulder compliments Scully on the realization that Nemman didn't do the autopsy on Swenson he is driving with his left while his right hand is used to pick sunflower seeds. In the next shot, Mulder's hands have switched. Now he's driving with his right and using his left for the sunflower seeds.
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 Mulders left.
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.
Mulder and Scully are standing out in the rain when Mulder tells Scully that Billy Miles brought the others out into the woods. In the next scene, at the hospital, it is daytime, sunny, and both Mulder and Scully are dry.
When Scully is entering info on her laptop about Soames's autopsy, look closely at her computer screen. You'll be able to see that the monitor is CRT (cathode ray tube). CRT monitors are only found on desktop computers and not laptops.
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.