This is a bit of a synchronicity exploit that you or the AI can use at times. Say you're fighting heathens and you get your holy order on the field. Now if you somehow become involved in another war by answering a call of arms or suddenly some other war falls on your lap, the game still allow you to use the previously raised holy order/orders in the new war even if they're against realms of the same religion. I believe this to be an oversight. Maybe in this kind of situation the holy order should be considered neutral against the same religion realm but you can still use them in your original war against heathens. In order to fight the same religion realm you'd have to use your own troops.
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