Brother Simon Damien is shown holding a pen in his left hand, but the position of the quill in the scenes where it is writing indicate a right-handed grip.
The climactic cathedral showdown between Lord De Guise and Nicholas has many discontinuities and a moment where De Guise speaks when his mouth is shut. This is a deliberate artistic styling to make the scene disturbing and disorienting.
Writing with the left hand was considered a sin in the Middle Ages, and would never have been taught to a monk. But Simon Damian has learned of his own accord to do it when nobody is looking.
The troupe of actors is heading north, as they tell Nicholas at the campfire, but when they come to a collapsed bridge shortly afterwards and debate whether to go west or east along the river, they point to their right as being west, which is the wrong way round.