Another bug I noticed:
Sometimes I am given a mission to destroy a ship, but I can't seem to find it anywhere on the level. I have had this happen a few times, so I searched carefully at every planet to try to make sure I didn't miss it. I am pretty sure I was thorough and didn't let anything get past me. At the end of the level, it says I failed the mission.
IIRC, when the bug happens, the mission is first offered, there is no image for the targeted ship (usually it shows a picture of the ship when you are first given the mission).