The Crusades are probably the best example but there has always been conflict between catholic and protestant - read up on the spanish inquistion (not the Monty Python version!) and the effects through Europe.
Of course we had our own versions throughout the tudor and stuart reigns in this country and of course there has always been the problems more recently in Ireland.
Also more recently (1947) there were considerable religious problems in India after partition (Hindu & Muslim).
Many of these have repercussions today.
In fact most of the problems with wars back in history seem to have religious connections so you shouldn't have to look far!