Mistake adds depth
Fairly early in the film, the young hero Paul gets into an argument with the Monsignor. Though I don't have the exact quote, Paul says something to the effect of "I'm an atheist! I don't know whether God exists or not."
Now, it seems likely to me that this confusion between "atheist" and "agnostic" is just a slip on Anthony Hinds's part. However, it adds a charming depth to Paul's character. He is a student, after all, and this slip up shows that he is the type of student (probably just as common in the 19th century as in the 21st) who has been educated beyond his intellectual capacity. He wants to be heard using the word "atheist," so people know how smart he is. Paul's real education comes later in the film, and by then, for him, the difference between "atheist" and "agnostic" is rather a moot point.
Sometimes a blunder can be felicitous.