The Gospel of Thomas is a real historical document that some believe to be the actual words of Jesus to his disciples; however, the real-life document was written in Coptic, an ancient Egyptian language based on the Greek alphabet, not Aramaic, as the movie states.
When Father Kiernan (Gabriel Byrne) comes in the Vatican office to get is new assignment, we can hear a bit of Italian speaking in the back between Cardinal Daniel Houseman (Jonathan Pryce) and another priest. Translation: "Rest assured, none of this will ever leave this room."
The house Frankie Paige is taken to towards the end of the film is the Filoli Mansion, located 40km south of San Francisco. The 1997 movie The Game also features the Filoli Mansion and both movies show very similar shots of its front entrance.