I took a protection mission (keep ship xyz safe for 30 days). I followed the ship around, even fighting off some other ships. As the time expired, the protected ship left the system and I was informed my mission was a success and told to pick up my reward. Before I went to pick up my reward, though, I was informed the ship had been destroyed. Even though the date had passed, I was given a failed mission status! Is this a bug? Is there anything I can do to fix it?

As for fixing it by editing a save game, not sure if that's an option. If not then you're stuck with:

- reload an old save. Lose all the progress of the past thirty days. Sucks

- go with it, and use it as a challenge to repair your relationship with whichever race / faction was upset by the failed mission.

- get pissed and swear a vendetta against that race. Pirate their asses off and get your money that way. Your relationship with them gets hosed badly but you can always fix that.

Also, in regards to the pirating thing, jail can be a fun experience in itself, and with a bit of work and luck (so not to be tried on high difficulty) you can even profit!