And here is my tip:
If ((troopTransportAutomanage == true) && (troopTransportFleet == none))
    then troopTransportLoadTroops == anyYourPlanet

High price of an strategic recourse from which your ships are made can create an economic crash (also for all AI). 

<t> I think i figured out what is causing this. Check if there is any resource from which ship are build whit higher galactic demand then galactic stock. High demand increase increase the price of the ships, bases etc. And ship prices increase maintenance cost. All because price of the goods is tied ...