Actually, friendlies shooting at each others does make a certain amount of sense. I think that what happens is that during a real furball, some ships inadvertantly hit a good guy instead of the bad guy they meant to hit, and the good guy takes offense to being shot at. Since the AI doesn't seem to distinguish between "generally" friendly and "generally" unfriendly classes at that point, I think the individual animosity is the only thing the AI recognizes and allows the battle to continue between two ships that should be friendly.
I've actually had this happen to me a couple of times, when I hit a merchant by accident during a battle. That ship still shows as blue (friendly) on my radar, but if you communicate with it, you'll notice that the available selection of messages for that one ship is decidely less friendly than it is for other merchant ships that are in the area. So, it appears that you can have an individual enemy even though you are friendly with the class as a whole.