Okay, I dunno if this is only happening to me, but my boat battles tend to bug on me, depending on what choice I choose. When I choose the option to charge in and board the enemy boats, everyone ends up being an enemy. If I choose the enough planning and head to battle, where I don't start boarded on the boats, it works just fine. Like, while I was enlisted in Stannis's army and he'd engage the sea pirates. I'd follow him into the battle and everyone will end up being my enemy. So either I murder them or they all murder me.
Ok thanks for reporting, ill take a look at this. Any more info would be great. What other options do, what happens in freelancer etc. I only need to look at the code and mission templates thats bugged then :).