Not a bad game, but it seems like there's a bug in the Research tree. Silica Binder Refining seems to have a prerequisite technology that doesn't exist, or isn't on the tech tree yet.
Congrats for making it through all three modes! Prestige mechanics are not really implemented yet, want to get the basic gameplay right first.
The research center bug is already fixed for the next update, there should be unlimited upgrades now. The carbon discovery is not triggered indeed, it should happen once you scan your first system with carbon, will take a look.
What did you think about the gameplay mechanics in the later stages of the game and the transitions between them?