Did you also fix those planetary tile bonuses that don't do anything? Like the "Caverns" tile which gives +3 to Resistance? No structures receive any bonus from Resistance; my guess is that is supposed to be +3 to ship construction. There are several others that similarly don't provide bonuses to on-tile or adjacent structures, or structures that don't get any level ups from things that are supposed to provide bonuses to them. This is particularly bad with social construction, all construction, and ship construction structures and tiles. One specific structure I can think of off the top of my head is the synthetic (or Yor) Production Center structure (the first level manufacturing building); it can be like level 5 from adjacency bonuses which still gets it an amazing +0.0 % to all construction.
I keep hoping that someday I will start playing a game and not encounter broken tiles and/or buildings...
P.S. Oh and there are still a lot of anomalies that say something to the effect of "your research increases by leaps and bounds", but you gain absolutely zero research.