A lot of people are being dismissive of the problem, but I think they're being a little too forgiving here. It's easy to say "just watch your fire", but when you're in an intense fire fight with a hostile, you find yourself within less and 1 km and then BOOM a police ship flies out of no where right into your line of fire it's hard to not hit them by accident. If I were in that police ships position, and a friendly human player hit me I wouldn't instantly turn on them, I'd tell them to watch it at least a few times (and apologise for flying into their line of fire).
That would be sensible. However I don't think it's likely to change, despite people complaining about it for months. It would also be nice if they prioritised the higher bounties, but no apparently one friendly fire incident and I'm much more important to kill than that pirate with a five figure bounty.