Corrected entry: At the crash site of Flight 549, Scully says "The plane came in nearly vertical at 300 miles per hour." yet the fly-over view of the debris field shows it spread out over hundreds of feet. Unfortunately, on 9/11 we learned when large commercial aircraft crash straight into the ground, they leave massive, smoking holes. First responders at Flight 93 were not even aware they were looking at a crash site.
Corrected entry: Up to this point in the series, Samantha has been shown by the Smoking Man to Fox. In this episode it appears Fox has completely forgotten the fact that he already saw his sister alive on more than one occasion and appears to back on the belief that she's missing and has accepted the fact that she is dead.
Corrected entry: When Mulder, Scully and the other police officers are digging Ray Soames's grave, one strap of the coffin breaks and the coffin falls and starts to roll. When it hits a tombstone and opens, you can see there's a normal size body in the coffin. When they look into the coffin, there's this small alien body. (00:13:35)
Corrected entry: In this episode, Mulder and Scully are watching a film about them that was shot sixteen months ago. But that would have been sometime in late 1998, when Mulder and Scully were not on the X-Files. But yet they're in Skinner's office at The Beginning. If they had shot the film in consistency with the current timeline, (2000) then the film would have been shown in late 2001. But in that time, Mulder was missing and Scully had a newborn. if anything, she would have seen the movie with Doggett. Somebody didn't plan ahead... (00:04:05)
Corrected entry: 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. (00:02:20 - 00:04:35)
Corrected entry: Mulder takes out spray paint from the trunk. The problem is that the car isn't his but it was rented. It’s not plausible that all the cars in the rent-a-car company were equipped with spray paint. It is also doubtful that Mulder anticipated the paint use and bought it on purpose. (00:10:40)
Corrected entry: At The End of the season 1 finale, The Erlenmeyer Flask, CSM is seen placing the alien embryo (pickled in a jar) in a box somewhere deep in the Pentagon's storage facility - yet in season 6's One Son, the embryo is back in the flask, in the freezing solution where Scully found it in the first place. (00:30:35)
Corrected entry: The tv-esque footage of the show is supposed to be being recorded as the investigation goes on, it's not pre-recorded or supposed to be airing as we watch, yet there is a perfectly placed 'blur circle' following the face of the prostitute. That kind of thing is generally done when filming is done and being edited for tv; even if for whatever reason they decided to blur her face during filming, the blur point follows her face perfectly despite her flailing and panicking, which is highly unlikely.