Not sure if I'm doing something wrong because I have to wait a super long time for only circuits or research points to continue with the game. I can make 1000s of ships that don't use circuits but I can't conquer planets with them
Resource rate for shipping are inaccurate. Planets that claim to be importing slightly more than they are using will run out rather than accumulate that resource.
If all of your heroes are scared at the same time, they will retreat automatically.
If all of your heroes are under enemies control at the same time, the battle is lost.
That's intentional for this scenario, see the story messages that pop up. But maybe I should clarify this when you try to build!