A Tatar raider mocks the idea of the virgin birth of Jesus. Belief in the immaculate conception is actually a tenet of the Islamic faith.
After Rublev comments that nothing is more terrible than snow falling in a temple, some of it lands on Durochka's hair and is clearly a white feather.
In the final scene, set in 1424, Rublev vows to paint an icon of the Trinity. This icon was executed in 1410, 14 years earlier.
The smoothly-cut logs that feature many times in the early scenes are clearly cut with machinery not available in the early fifteenth century.
A woman is seen swimming past Andrei's boat using the front crawl technique. This technique was only introduced to the European continent in the latter part of the 19th century.
During the crashing of the self fabricated hot air balloon at the beginning of the movie, two, not so 15th century, buses are seen.
The film begins with a manned hot air balloon flight taking place in Russia in the early 1400s. There is no evidence for such an event. The first manned flight of a hot air balloon did not take place for several hundred years, and the inventors were not Russian. The French brothers Joseph-Michel and Jacques-Étienne Montgolfier are credited with this accomplishment, with the first flight taking place in France in 1783.