When Charlie's father hands the ice cream to him there is one scoop of ice cream, but in the next shot there are two.
When the car window breaks, it splinters like plate glass instead of shattering into beads as safety glass does.
Mulder refers to the Swastika as a symbol used since the middle ages when in fact it has been used for thousands of years, appearing as early as ancient Greek pottery.
Dr. Charles Burk refers to the biblical story of Jesus multiplying the loaves and the fishes as an example of something materializing out of thin air. Scully responds, "Yeah, but that was a parable." This was not in fact one of Jesus' parables, but a story of a miracle that he performed. The stories of Jesus' miracles are very easy to distinguish in the four biblical Gospels from the parables that he himself narrates.
Mulder also refers to the Swastika as an inverted Swastika. This is not the case. As we see it, the cross is represented the way it has been for ages, it's the Nazis who inverted it.