What was the main practice of the church that Martin Luther disagreed ?

It is hard to break up. I would say the biggest thing he rejected was the concept of the pope. He has a major problem with the idea that people needed an intermediary to connect with god. This is reflected in all of his grievances. selling of indulgences and communion, etc. For example both of these require the pope, or an agent of the pope to do something to communicate with god on behalf of people.