Game patched to 1.02.018
1. The Gaian Crescent scenario your initial planet starts without any infrastructure built upon it. So the scenario starts with 35% max allegiance due to no home planet and negative cash flow.
2. If you have a negative fleet supply you will not build any vessels even if you should be able to produce a few. This is testable by queueing up multiple fleet supply techs and then queue up more ships than the first technology gives.
Example: I have zero fleet supply points available and I queue up the next 2 techs which give 150 points each. I then queue up 300 points worth of ships. You would expect 150 points worth of ships to begin construction once the first tech is researched. However no ships are produced until both techs are completed and your supply reaches zero.