Continuity mistake: We see Cindy and Teena at the table talking with Eve 7, drinking out of paper cups. Later on, when Mulder picks up a cup from the table, it's made of glass. (00:30:40 - 00:34:30)
Continuity mistake: When Dr. Kendrick/Eve is talking to the two little girls and she's clearing up the mess on the table, the position of the straw changes between shots. (00:29:55)
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"). (00:02:15)
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. (00:22:40)
Character mistake: Scully gives a description that Eve is driving a Blue Carolla. However in the next scene, Eve is driving a Pontiac, not a Toyota. (00:28:00 - 00:28:51)
Continuity mistake: When Mulder grabs the twins, one of them immediately turns around toward him, however in the next shot she turns around once again. (00:41:10)
Answer: As he stated many times throughout the series, Mulder needed Scully to be sober and skeptical. Whenever Scully's skepticism wavered and she started questioning her own rationality, Mulder would try to restore her sense of skepticism, because he needed her to be clear-thinking.
Charles Austin Miller