One bug I saw in 3c that kind of messed up a good start for me. In one game I was playing, the Iconians built a mining starbase on a couple of resources. But it didn't show up with the screen zoomed in. When my constructor got there, I just couldn't move onto the resource square. Zooming out revealed a base had been built. But in zoomed in mode, the base just wasn't there. (My constructor was right next to it. So there was no fog of war).

Reloading fixed the problem.

I was alt-tabing a bit to write an AAR, so maybe that affected it. Not really sure.
I suppose it's possible there could be invisible other types of bases. I'd just never know about them because I'd never try to move onto some random square.