I've noticed that, with every weapon except for one, friendly AI ships are pretty good at not shooting their friends and/or you.
That one, however, is the Tachyon Lance, and it can end your day rapidly. I usually end up taking more damage from my own fleet than from the enemy when running multiple Tachyon Beams in one engagement.
Is this an easily-solved AI issue, or is it sort of a balancing consideration to the Lance's power to knock out frigates and fighters at ridiculous range? I'd love to see it fixed, as while it's an interesting balance consideration, it's really annoying and doesn't make much sense from a "fun" perspective.