In the motel guest death scene, when the other guests enter the room, the deceased man's eyes are closed. When Mulder enters, the deceased's eyes are open and looking around.
Near the end Fox is eating a piece of cake or cookie, he is picking up the same piece twice. In between shots of the first and second time, it shows that the plate has nothing on that side of where he picked it from the second time.
Scully tells Mulder that "...the flush toilet was invented by a man named Thomas Crapper..." This is an urban legend that has a ring of truth. There was a man named Thomas Crapper (1836 - 1910), and he was a plumber who founded Thomas Crapper & Co. He made a number of useful improvements to already existing flush toilets which did much to increase their popularity. However, the invention of the flush toilet itself dates back to 1596 and the first British patent was granted in 1778. Another urban legend is that the words "crap" and "crapper" (the latter meaning toilet) derive from Thomas' last name, but both words were in use before he went into business.
The Sheriff states that "Killer bees are a government experiment gone awry," implying that the US government was involved in transporting African bees to the Western Hemisphere. It was the Brazilian government that did this as early as the 1950s; the African bees escaped captivity, bred with native bees, and it's their descendants that have migrated North from there.