javic12: (And as I recall my sneak attacks were always against bad guys who would attack me if they saw me first.) 
  Too late to help you if you've finished your playthrough, but I'm nearly certain that this is the source of your bounties then. I still haven't played Nehrim, but in Oblivion itself, there are a number of NPCs that will instantly turn hostile and attack when they see you (mostly certain NPCs that are members of Mythic Dawn, if I remember right, but there may be others), but if you sneak attack/kill them 
before they turn hostile, then it counts as a crime. As long as the hostile switch gets flipped first, then you're defending yourself, which is allowed under the crime/bounty rules, but you lose the ability to do the sneak attack in that case. 
I do remember that I got in the habit of steering clear of guards and/or making sure I had enough money to pay the fine if/when they caught me (I don't like going to jail with the associated penalties). 
 
 I do clearly remember at one point being stuck when I needed to chat with an NPC to advance a quest. I had a bounty on my head (reason unknown), and a guard was patroling near the NPC. I also had almost no money. So I abandoned the current quest and went off to do other things until I had more money, then returned and continued, got caught, paid the fine. Not a great way to play, but doable (and perhaps "realistic" if you think of my character as a habitual criminal who never has any money :-). 
 
 Maybe not the most enjoyable way to deal with the situation, but as you say, certainly doable, lacking any real alternatives. :)