After drinking from the contaminated well, several characters immediately fall ill from plague. Plague by any vector has an incubation period of at least one day.
Sir John Hawkwood is depicted as being alive in 1501. However, he died in 1394, 107 years earlier.
When Martin is submerged in the poisoned well for several hours, he later comes out unharmed. In reality his skin and membranes should have picked up some of the poisoned water and he would have contracted the plague also.
After drinking from the contaminated well, several characters immediately fall ill of plague. Plague by any vector has an incubation period of at least one day.
The escapee girl from the castle is said to wear a "cross of gold". However, if you take a close look right before she is addressed, it is clearly made of two bars of mirror.
At the end of the film, a flaming ceiling beam falls and bounces in a way that belies its ostensible weight.
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 terms "scientist" and "science" were not coined until the late 19th century. At best Steven would have called himself a "natural philosopher".
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 Nicolaus Copernicus (1473-1543), Galileo Galilei (1564-1642) and Johannes Kepler (1571-1630) first proposed the model of the heliocentric system.
The movie is set in 1501. When Arnolfini's son talks about Da Vinci having studied the flight of birds, he refers to Da Vinci's book "Codex on the Flight of Birds". This book was not published until 1505. He could not have known it.
In the opening sequence, the Cardinal is serving communion in 1501. The "Flesh of Christ" he's handing out are modern communion wafers.
Toward the end of the film, a bright set light seen reflected in Summer's sword blade.
In opening scene, a camera shadow is visible on the Cardinal.