The crusade was a lengthy and messy campaign, and things are prone to go bad occasionally. No matter how much you prepare, there is always something, someone who just can't follow the rules and makes it their life's goal to abuse the little power they are given.
Since the crusade also involved the knights and wizards from various kingdoms, the second sons and the useless ones, some units of crusaders sometimes did things that the church would never avow to. Although the leaders of each unit were church members, when nobles entered the fray with deep pockets, things tended to go out of control.
And… consequences to this, the innocents suffer—believers, someone's father, daughter… someone's mother… they suffer.
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Ender Village, Duchy of Ironstone in the Gracia Kingdom.