They often were. A lot of history has been retold more in a way to fit contemporary narrative than to maintain historical accuracy. For instance Galileo. The typical tale is something like Galileo dared claim the Earth is not the center of the universe, the Church freaked out at the violation of dogma, shunned him, and he was lucky to escape with his life. In reality the Pope was one of Galileo's biggest supporters and patrons. But they disagreed on heliocentrism vs geocentricism.

The Pope encouraged Galileo to write a book about the issue and cover both sides in neutrality. Galileo did write a book, but was rather on the Asperger's side of social behavior, and decided to frame the geocentric position (which aligned with the Pope) as idiotic, defended by an idiot - named Simplicio no less, and presented weak and easily dismantled arguments. The Pope took it as a personal insult, which it was, and the rest is history.

And notably Galileo's theory was, in general, weak. Amongst many other issues he continued to assume perfectly circular orbits which threw everything else off and required endless epicycles and the like. So his theory was still very much in the domain of philosophy rather than observable/provable science or even a clear improvement, so he was just generally acting like an antagonistic ass to a person who had supported him endlessly. And as it turns out even the Pope is quite human.