Factual error: The priest says that St. John saw the number 666 in his vision, but it was actually 999 inverted. I'm not sure, but I don't believe St. John read modern Arabic numerals like we do. Didn't he read Roman numerals? I think if St. John saw the number 666, it would actually be DCLXVI.
Continuity mistake: In the scene were Arnold disconnects the carriages of the train, near the end, he has to jump across the gap. When we first see the gap it is a certain distance, the camera angle changes and it's a bigger gap, then the angle changes and it's closer, there is no way Arnold could have jumped that big gap.