I have the CD-ROM Classics version of Privateer, and some of the missions just turn out incorrect for some reason. It's a rare occurrence, but I've had missions where I'm supposed to go up against retros or pirates and found Kilrathi waiting for me. I've double-checked things and the mission description clearly states that I should expect either of those human threats. Saving and reloading with such a mission active does not change the enemy in any way. I have a saved game from before one such mission if anyone wants to see for themselves.