Updates (all from after the patch that was pushed yesterday, same save file, game still presents itself as Alpha .40):
bug 1- I'm now realizing that Chimeric Biomass adds only one to the planet value because it adds one food production. My bad.
bug 5 (the shipyard sidebar displaying the wrong work in progress) seems to be fixed after reloading.
Now for new issues noticed:
Lets call this Bug 1, part 2. I got the Chimeric Biomass again, used it on Earth, again, and I could have SWORN it only added one tile, not two. However, I do not have a save because I save scummed after getting a colony ship blown up, my apologies. Later uses of a Chimer Biomass (on a different turn) did properly add two tiles.
Bug 6. My second starbase, right when built and then assigned to be an economy starbase, was displaying the option for the Xeno Archeology lab, despite having no valid targets in range. I suspect it was 'grabbing' this choice due to the fact that my first starbase, a mining base, did indeed have valid targets for a Xeno Archology lab, but due to a lack of modules I had not built it yet. This option eventually disappeared, I did not notice exactly when, apologies.
Bug 7. The Ysenguard - Multiple bugs. First, it claims to be a survey ship, but it has no survey module. Could this be bacuase I did not have the tech for Survey Modules when I got the event and built the ship?
Ysendguard part 2, it claims to be a prototype, and should be earning XP each turn, but I have not seen earned XP each turn.
Further info: When going into the detailed ship screen page, and hovering over the components in the top right hand corner, the prototype component is not displaying values properly (text overlapping with icons and fading out, so it's incomplete), and there is a component just labeled 'Component', perhaps that is where my survey component should be?
Bug 8. When in the planet view, about to rush construction on something, the popup on the rush command said I had 1631 credits, the bar at the top of my screen said 1630. Rounding error of some sort causing the discrepancy?
One final issue, maybe a bug, maybe an oversight, maybe it will be implemented soon, maybe working as intended: got the tech which allowed me to build trade freighters, built one, went to send it to another 'player's' planet, and got an error saying I have no trade licenses available. Ouch! I need that income! 
That's it for bugs for now. I'll try to do a post with other thoughts and feedback soon, but doing such a post properly will take a bit of time.