A friend and I have both been having bugs with our bounties on our alts. We racked up pretty high bounties (about 300k - 400k each), and they have not gone down at all in a few weeks.
When I logged on my alt with the bounty earlier today, the bounty had gone down to about 269k. I thought, well, that's not bad. But halfway through grinding my alt, when I had done no crimes or been anywhere near guards or innocents, I noticed my bounty was back up to 320k. By the end of grinding, a few hours of crime-free playtime, my alt's bounty had gone back up to 370k.
My friend logged on her alt to grind with me, and sure enough her bounty began to do the same thing. Every time we entered or exited an instance, our bounties rose significantly.