Factual error: Scully reads to Mulder from a book all about flukes (Trematodes). However, the information she is quoting is wrong. She states that flukes or flatworms have a "scolex" with hooks and suckers. These are actually the distinguishing characteristic of cestodes (tapeworms). Trematodes have no scolex and definitely no hooks.
Continuity mistake: After the part where the head Kindred woman tells Mulder and Scully "I asked you not to interfere", Mulder leads Scully away. From one camera angle, he is leading her away by the hand. In the same scene, but from a different camera angle, he has his arm around her. When we go back to the first camera angle, he is once again leading her away by the hand.
Continuity mistake: In the mine with the medical records we see Samantha's file. In the season 1 episode "Conduit" we see the X-File Mulder opened on her. In the previous episode she is listed as Samantha T. Mulder and her birth date is 1/22/64. Here we see her name as Samantha Ann Mulder and her birth date as 11/21/65.
Continuity mistake: When Scully is reading report from Simmons' death, we can see that is has occured on the 7th of November, 1993; which means that whole episode takes place at the very beginning of November, but at the same time Scully and Mulder should be at Alaska (see episode "Ice").
Continuity mistake: When Scully is talking to Skinner in Mulder's empty hospital room, her cross necklace is off to the left. Then, when she says, "Sir." it's almost centered. And no, this was not caused by her turning around a minute or so before she said it.
Continuity mistake: 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 tomb stone 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.
Factual error: At the crime scene where Roland killed one of the professors by dunking his head in liquid nitrogen and dropped him on the floor, someone has drawn an outline of the dead prof's body and all the bits his head broke into when Roland dropped him. This outline-drawing doesn't happen in life because it interferes with the crime scene, it's a popular myth.
Factual error: When Mulder gives Scully the birthday card, she says that he is two months early. Given that Scully's birthday is on 23 February, the time of the episode should be sometime near Christmas. However, through the whole episode, there is no sign of Christmas time (not a single Christmas tree, no Christmas decorations, etc).
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.