Just before Ephesian and his followers are released, Mulder is in an interrogation room with Melissa. In the shot from behind her, Mulder's hand his on top of her hand. It switches to a shot from the door behind Mulder and his hands are not near Melissa's. It switches back to the shot behind Melissa and his hand is again on top of hers.
When Mulder is interrogating Ephesian he references the "Church of Ephesia". The correct name is the Church of Ephesus.
In the beginning of the episode, Scully correctly refers to the book of Revelation. Then in the last ten minutes, in a discussion with Skinner, both Scully and Mulder incorrectly refer to it as the book of Revelations.