I've encountered a couple of situations with missions in which the game has been unable to respond to the outcomes.
1) Delivering water ice to a Commonwealth settlement after I'd accidentally wiped out one of their defence craft with a stray shot or two. I was unable to dock, and thus unable to complete the mission. Finally I had to go elsewhere and sell off the ice and return, whereupon I finally got a mission failed response. I did not, however, get back the cargo that had been taken out of my ship when I embarked on the mission.
2) Accidentally wiping out a Sung slaver with the Shatter power and leaving no wreck. I was on a mission for the Huari, who refused to believe that I didn't have 17 slave coffins with me. That one was ultimately unresolvable and I had to leave the Huari be and move on.
