In the last Conflict Zone I fought in, I was chasing down an enemy attempting to flee. I had two allies on my tail pursuing the same target - I was slightly faster than them, so stayed ahead, and they kept shooting me in the rear, thanks guys!
Anyway, I finally catch this fleeing foe (he was in a Viper, me in an Asp) after lots of boosting and take him out - he'd already been badly damaged by me before he tried to flee. The moment of his destruction, the "allies" following me turn RED and attack me and I get a Bounty in the system...I'm guessing I must have flown beyond the bounds of the Conflict Zone or something - not that this is mentioned at all of course. Still, a bit bloody stupid! Note: considering my top boosted speed is only about 360, I'd not flow particularly far away from the main action. Plus the other guys were still shooting at this guy, though they were out of range (of him) and tagging me regularly with their shots.
So yeah, my rep got hammered while I was attempting to improve it as the game considered me a murderer for taking out this particular foe - a foe who'd previously given me a bit of a pounding which was why I was so keen to take him down. Basically blew about half my earnings to clear the false bounty on me. Lovely.
The thing I find odd about missions in conflict Zone is you can choose either side when you arrive, not just the one you signed the mission for, yet you still get paid even after joining the "wrong" side.
Scoob.