In the Middle Ages there was a lot of conflict within the Catholic Church.

First came the Great Schism in 1054, where the Eastern Christians split from Western Christians over Eurachism. Yeah. The thing where you eat wafers at Church. That's actually why they split. Also use of a pope and saints, but it was mainly the bread. From there, more divisions grew.

By the 16th century, the Catholic Church was extremely corrupt. Being a powerful political entity for so many years, the Church started getting underhanded. It started suppressing ideas that countered not the Bible, but the Church, under threat of execution. For example, Galileo was put to death because his findings contradicted the Chruch's acceptance of the heliocentric model, and when he recanted he was placed under house arrest for the rest of his life. Being labelled a heretic was worse than death. Then, indulgences. The Church began saying that if you payed for confessions, you were guaranteed a seat in Heaven. Martin Luther finally spoke out about this, and was labelled a heretic and excommunicated. This started the Protestant Reformation, wherein the Protestant, Jesuit, Franciscan, Calvinist, etc. branches began forming. They all broke away from the Catholic Church and promoted reformed interpretation of Christianity.

Eventually, the two sides reconciled, but the divisions were never nullified, and still continue today in peaceful coexistence.