When they are in the garage about to leave, it is night time; when Mulder goes back for John, it is day with full sun.
The Son is shown locked in a room with a single window facing the rising sun. As the sun comes up, he is gradually backed up against the opposite wall as he tries to avoid the shaft of sunlight. But a shaft of light from the rising sun would progress downward and move away from the opposite wall, not toward it.
In an early scene, the words "John 52:54" appear written in blood on a wall. Mulder acknowledges the Bible reference and quotes the verse. However, the Gospel of John only has 21 chapters, and the verse Mulder quotes is actually John 6:54.
When Kristin pours the gas, she pours it from the garage to the kitchen, then lights it on fire. A second later, Mulder sees the house explode. Gasoline that is not in a sealed container will not explode.
When Mulder is looking at the police reports, the one for Portland Police (Oregon) is mislabeled. It says "Portland Police Department." Portland's police force is actually known as Portland Police Bureau (PPB).
At 6min 38sec Mulder removes the sump cover twice.
Correction: There were two sumps - the first one empty and the second one containing the red (bloodied) water. When he removes the second cover you can see the first one at the top right of the shot.