I am bumping this because I am having the same issue (as is everyone because the mercenary feature is obviously broken). This is not listed as a known problem by the devs though which is quite frustrating to me. This is a MAJOR feature of the game and it is just so obviously messed up. Something about the pay for being a merc is obviously working, I am rich, but I'm not sure where a lot of my money is coming from. Can I track minor events like income like I could in Warband?
How do you not catch that there is no way out of a mercenary contract without making the faction hate you... OK, fine, you missed it, embarrassing but understandable. Its the fact that they still haven't added it to the known bug list. This isn't a single broken quest that you can break if you do just the right thing. Its a massive feature of the game!
I really am loving the game as a whole. The lack of awareness of such a large problem does concern me as to the future of the game, though.