Factual error: Mulder sees water going down the drain counterclockwise and says something is up since all water in the northern hemisphere drains clockwise. This is not true. Water can drain in both directions in both hemispheres. Things like convection currents, basin design, and residual swirl from filling the sink have a much greater influence. You would have to drain a small ocean to see the Coriolis effect, or use specially-designed test apparatus. See http://www.snopes.com/science/coriolis.htm and http://www.physics.ohio-state.edu/~dvandom/Edu/newcor.html (scroll down to *5.2. Water Going The Wrong Way Down The Sink* near the bottom of the page).
Factual error: Mulder mentions the USS Eldridge as disappearing from Philadelphia (and later reappearing in Norfolk) "nine months after Roswell", i.e., May 1948. In fact, the supposed incident took place much earlier - in February 1943, according to almost all reliable sources. (00:06:50)
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. (00:17:30)
Factual error: In the opening sequence, we see a nuclear attack submarine beneath the ice in the Arctic Ocean. When the captain orders the ship to surface, one of the crewmen mutters, "Surface to what? We're under 32 feet of glacial ice!" Except that they're not under "glacial ice," they're under Arctic sea ice, which ranges from about 6 feet thick in the summer to about 15 feet thick in the winter.Charles Austin Miller