Thanks for your feedback, Paolo! I think you're basically right about causes vs. effects, though that's different from how I conceptualized the distinction. Scenarios (as well as major complications) represent the major problem facing the characters - why is the clock ticking as they drift out in space? Broken systems represent problems they have to solve before they can succeed (of which at least one should relate to the scenario). And dangers represent additional obstacles that you can leverage for complications and challenges while they are trying to get the ship going again.
If you get a chance to play Stuck Out in the Black, please let me know how it goes!