TEC Torpedo ships-damage is dealt immeaditely after use of ability, rather than timed with the impact of the torpedo. normally this is not a noticable lag, due to combat, but it was disconcerting when his starbase blew up several seconds before my last salvo of torpedoes impacted.
This isn't a bug, it's just how the engine works. This wasn't really as noticeable before because weapon fire is quick enough and most damage abilities were near-instant so now this sticks out like a sore thumb. 
TEC Starbase- also, I don't know if this is supposed to be, but are we really allowed to build starbases in the star's gravity well? just asking
Yes, this is intended!
AI- This may be because I was playing against an easy AI (TEC) to get used to the feel of the new toys, but I found that the easy AI, while building starbases (in random, not particularly important systems) never in fact upgraded them to my knowledge. Granted, I can't tell if it has the docking bonus upgrade or the frigate shipyard upgrade, but they never upgraded defense or fighter base as far as I could tell. again, may be b/c I'm facing easy, just wanted to make sure.
The AIs in general build more than they upgrade. They tend to build a bunch of barely upgraded bases rather than a few fully upgraded ones.