One of the greatest controversies of the Renaissance would be the idea of Humanism, which is the idea that humans can be good people. The church leaders at that time didn't like this idea because they didn't have the power over people that they used to have when they could say, "God hates you because humans are sinful, so you have to do everything we tell you to gain His forgiveness," and other stuff like that.
Hope this helps! Please let me know if I'm wrong :)