I've noticed on a few occassions that members of my party will turn on me after a battle. Is this to do with their alighnment or am I missing something. I hate to have to kill them, but I don't know what else to do.

You're probably damaging them with AOE spells, NPCs can turn hostile if they think you're attacking them. Or maybe they've been dire charmed or confused by a spell.

So what's an AOE spell?

Area of Effect spell, which affects an area rather than an individual.

This happened to me as well. If they are not
being affected by a spell and they are attacking you or each other, try this: hit the select all button in the bottom right corner of the screen, when the formation choices come up across the bottom choose the "x". This worked for me. Unfortunately i died once or twice after narrowly winning a battle because of this. Nothing worse than mutiny causing you to re fight a battle.