OK, I've fired up a new game here, and already I've encountered several (unfortunately).
Precursor Worlds DLC: I just settled a Promethium Refinery World. It's supposed to give me +5 Promethium when I do so. It didn't. It wasn't like there was an option in the colonize event that should have given me this, it's supposed to be just the basic bonus. I looked at the XML, and it seems that there's a Flat bonus of 20, but the target is Planet?
Ship maintenance is totally borked. It seems that all my ships have a maintenance of 1. That's regardless of what the actual maintenance should be, based on components. Also, the Maintenance number for a ship (as shown in the Designer) is wrong - it's always set to 0.
Another thing: the Colony Module's maintenance is set to 23! At least according to the Designer interface.
Looking at the XML, I don't see a Maintenance entry for anything in the ShipComponentDefs.xml file. Did we give up on maintenance costs for ships in favor of only requiring a flat 1 per ship? When did that occur? If so, then the Designer needs to be fixed. If not, where are the Maintenance costs for components being stored, and why isn't the total being calculated appropriately?