I am new to Space Crusade and I get the idea (similar to HeroQuest) that the GM as GM has final say (but he should not cheat for his own benefit since this is more competitive than heroquest!) but...
In the first mission (Spoilers) the secondary objective is to kill the one Android. The points for failing at this are not forfeited unless the secondary objective is revealed (via the Alien Event deck) and no good guy faction accomplishes it.
Here is how I would handle it. If the Android is killed but the card not revealed, it's just like killing a regular Android. But if the card is revealed after the fact, that faction gets the bonus points for the Secondary Mission retroactively. Maybe others would say it only counts if they got the card FIRST but the Android might end up in the first room (that happened to us) and the Card might not be drawn until the very end (or not at all).
I realize too that when the last Alien Event card is revealed, the good guys have only one final round of turns to accomplish their mission(s) and leave or else Chaos automatically wins!