Pfefferkorn said that he received a letter from Ulrich von Hutten about his healing of syphilis. The story takes place in the late 1520s, in 1527 to be exact, while Hutten died in 1523, most likely from syphilis itself. Futhermore Paracelsus couldn't meet him later in the movie. However they met in real life in Ufenau, where Hutten died.
During the movie Paracelsus is called by his nickname Paracelsus. This name however added by him in 1529, while the healing of Johann Froben, which happened in the beginning of the movie happened in 1527.
The Magister said that if Paracelsus would be a good doctor he himself would be "Hanswurst", later confirmed by Hans Pfefferkorn, a famous old name for a fool. While the name first appeared in Central Lower Germany in 1519 in the book "Ship of fools" by Sebastian Brant, it wasn't as popular in everyday's conversation until Martin Luther used this insult in 1530, which is a few years after the plot's events.
Paracelsus said that letting people into the city would be a "pranks of the citizens of Schilda" (Schildbürgerstreich). This term didn't enter the German language until it was first released in a book about the "Schildbürger" in 1597, almost 50 years after the setting.
Paracelsus mentioned that he mostly studied with the gypsies and on the street. However in real life he was taught by his father Wilhelm. Paracelsus wrote himself that his father "never left him" and he was thankful for the teaching he gave us. He later received his doctor diploma at the Ferrara university.
Johann Froben died from a while in coma, caused by a stroke, not by an untested drug, as shown in the movie.