Patricia Arquette's character is named Frankie (short for Frances), similar to the name of the saint, Francis, whom we're told by Gabriel Byrne's character was the first to receive the stigmata.
When we see inserts of the crucifixion, while Frankie as her first attack of stigmata, the arms being nailed are rubber arms with wires that make the fingers slightly move.
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 never leave this room."
The Gospel of Thomas is a real historical document that some believe to be the actual words of Jesus to his disciples; however, the real-life document was written in Coptic, an ancient Egyptian language based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 discussing the five stigmata, Frankie refers to the spear in Jesus' side as "the one that kills him." However, the spear was used to be certain that he was already dead.
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.
The Gospel of Thomas is by the Gnostic denomination which was founded in 125 A.D. and became virtually nonexistent after around 1400 A.D. due to lack of membership.