This is something that's been bothering me for a while, and I'd love to hear other people's input.
My biggest problem with games that offer you choices or have consequences for your actions is that they (almost) always assume your choices and actions were intentional. In Dragon Age 2, my LadyHawke somehow found herself having "girly fun" with Isabela and I'm still not really sure how that happened. In Oblivion, I got arrested for murder a lot* because of allies straying in front of my arrows - that's not murder! It was an accident!
But it's not something that I can see being fixed easily. How is a game supposed to know whether you did something intentionally or accidentally? The only real 'solution' I can think of is Fable's apology mechanic, which is less than satisfactory. I suppose you can sometimes get people to stop being hostile in TES by blocking instead of attacking, and you can get people to stop being hostile in Deus Ex by running and hiding, but both of those only really clear the immediate consequences; they don't satisfactorily allow for accidents.
Have you seen any other mechanics that help a game distinguish between intentional action and accident? How well do they work? Can you think of any other methods that could help?
* Before I started savescumming any portion where I had some stupid ally AI.