The fact that they have absolutely no understanding of even the basic principles of the faith. That they reduce the entire religion and all of the heavenly host down to essentially an army on the side of order in a battle between order and chaos. That they misrepresent the role of Yahweh, the angels, and pretty much the entire construct of the Church.
This is actually what ticks me off the most about the series, and why I really just usually quit the games partially through.