A ceasefire order from the Pope is not a two-way order. He can order one side in a war to stop fighting without issuing the same order to the other side. This often happens if one side has a higher Papal standing than the other. The better your standing, the more tolerant he will be of your actions. The lower your standing, the faster he'll slap you with the yellow card (love the choice of term, btw).
In your case, I suspect that your Papal standing was lower than Milan's. So, you go the yellow card due to attacking them, while the were given a free hand against you. Do you remember what both standings were at?
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