Thanks for the replies
I think people have slightly misunderstood me though, or I didn't get it across well enough. I meant to ask what is a good reason for loyalists to fight each other without one of them being "the bad guy?" It's tough.
It's easy to say "the marines are good, the inquisitor is a heretic" or whatever, but then the poor =I= player never gets to be the good guy, which is probably one of the reasons he picked that army in the first place. If I wanted my guys to be traitors I would have collected chaos instead of loyalist, and the same goes for my friend's marines.
It's just hard to think of reasons loyalists would fight where they are both still truly loyal. Mistaken identity is pretty much it.