When John Paul gives the Urbi et Orbi blessing after he is elected, there are 16 people standing on the balcony of St. Peter's Basilica. But in the following wide shot from St. Peter's Square, only two people can be seen on the balcony.
When the newly-elected Pope John Paul II is changing into his white papal cassock, the actor playing the pope switches between Cary Elwes and Jon Voight several times between shots (most likely this scene was filmed twice, once with Elwes and once with Voight, and the scenes were then edited together).
The WWII scene in Part 1 where Archbishop Sapieha is meeting with Nazi Gov. General Hans Frank where Frank reluctantly agrees to allow only twice-weekly Masses in Krakow's Wawel Cathedral in exchange for no more priests being trained and ordained is false. In reality, the cathedral was
closed by Frank's Nazis without any such bargaining and the previously ordained priests were to keep the Polish people uneducated, calm, dull witted and obedient to the Nazis.
After Wojtyla accepts the papal election, the cardinals rise and applaud. The camera then pans in towards the new Pope. However, if you look closely, it is actually the mirror image shot from the previous conclave, with John Paul I clearly in the middle of it all instead of John Paul II.