Got a very annoying pirate related problem. Getting your rep with pirates up takes an incredibly long time, and can easily be set back by random pirates attacking you before you get up to neutral (you'll lose 2-3 rep no matter what you do if they catch you). That's fine, makes sense. But it takes a lot of time and effort to get to neutral and above.
.....And then you try to run a procurement mission, probably for the pirates faction itself, and a raiding party spawns as soon as you enter hyperspace and attacks you. If you run away, you only lose a few rep, whatever. But, if your fleet is too large/slow to flee, you have no choice but to fight them -- which counts as a hostile action on a non-hostile faction and you lose 50 rep. I had to reload a save from like 3 hours ago to undo that, because I hadn't been saving :\