When Captain Hawkwood is announcing to the mercenaries that Arnolfini is reneging on the promise of reward, the cannons that he is standing behind, as if ready to fire them at the mercenaries, are 19th-century "parrot guns" used during the American Civil War.
There was no organized search for truth through skeptical thinking in the early 1500's. That came well after Galileo Galilei (1564-1642) and Nicolaus Copernicus (1473-1543) first began to question the teachings of the Greeks (Aristotle, Plato).
When Saint Martin's statue falls, impaling the Cardinal through the throat, the false skin panel covering his throat gaps at the top. It opens in a straight line and is obviously false and not just the skin pulling down from the force of the blade.
The goof item below may give away important plot points.
At the end of the film, Miel kills himself by running himself onto his sword which is pressed against a wall. When he falls to the ground, flat on his back, there is neither sword nor blood. When Stephen jumps over his body, again, no sword or blood.