Other mistake: In the scene where Mulder and Scully are first visiting Darlene Morris, there is a split-second shot of Mulder examining residue on his fingers that is edited in between Mulder and Scully ascending the steps to the porch and knocking on the door. It's as if the sequence was initially longer with Mulder discovering a suspicious substance before he and Scully knocked on the door that was not completely edited out.
Other mistake: Eve 6 says that ordinary human beings have 46 chromosomes, while the Adams and the Eves have 56 chromosomes. This makes 10 additional chromosomes. However, Eve 6 also mentions that they have additional chromosomes number 4, 5, 12, 16, and 22 - only 5 additional chromosomes.
Other mistake: After AD Skinner is finished being interviewed by the police, Mulder asks him about why he would employ the services of a prostitute. Skinner looks at him in shock and Mulder says "You didn't know she was a prostitute did you?" I find it hard to believe that at no point in the interview did the police not mention to Skinner the dead woman he woke up next to after spending the night with her was a prostitute.
Other mistake: Unlike Mr Chaco, who has the brace clamped around his neck, Scully is clamped around the top of her head, which is a quite irrational way of executing a person, because the clamp does not serve as a stabilizer. In fact, in this arrangement, Scully is not fixed to the stand at all.
Other mistake: When Doggett starts clawing at the freshly plastered wall, he does so at just below his eye-level and blood starts pouring from the hole he makes. The dead woman inside the wall was stabbed in the lower abdomen; there's no way that blood from the abdominal wound would've seeped through the wall at the level he was digging.
Other mistake: Deep Throat says that Mulder and Scully are standing in the very room, where "the first human-alien hybrid was created." However, only in the "Patient X" episode, are we told that it is Cassandra who has just become the first successful human-alien hybrid.
Other mistake: When Mulder is on his knees in the cafeteria talking to the gunman, there are several shots where you can see the sides of his jacket hanging wide open because of his raised arms, which would make the gun on his belt easily visible to the gunman as he talks to him, but he somehow doesn't see it until he goes to take Mulder's phone.
Other mistake: The surname on the envelope is "Szczesny" (which is of Polish origin and means "Lucky"), so its pronunciation should be something like "shtcheznhy." However, in the subtitles the surname is written as "Szezesny" and pronounced by Scully accordingly.
Other mistake: Padget hands over one page of his book to his imagined character who is invisible to anyone else except him. Therefore, the page should hover in the air for an external observer. However, Scully watches his apartment on a monitor and notices nothing strange.
Other mistake: In order to leave such bloody footprints, CSM must have stepped into the puddle of blood. It is impossible because the guy shot by CSM could not bleed so much blood in such short time, not mentioning that CSM must have intentionally stepped into it.