I only made it about 15 mins in, not sure if it autosaved... ill check. It seems like some fluke of the map because it happened twice on the same map with 2 different starting sectors, but I started a new seed with the same AI and they are behaving "normally".
Off topic suggestion... would it make sense for tractor beams to be able to slow down starships? I am playing vs mad bomber now, he has those replicating spinning blades that are immune to tractors and force fields... So each raid he comes in with a bomber starship and a couple dozen of those blades, goes right into my main base thru all the tractors and force fields and destroys all of my power plants and starship plants. Yay!
My suggestion, you should be able to set a tractor beam to focus on starships, it wouldnt stop them, just slow them WAY down so that your turrets have a chance to do something to them. Maybe mk 1 would slow 1 ship, 2 2 ships, 3 3 ships. While in this mode they cannot tractor smaller ships until you toggle the back over.
I know there are some other things that really slow down ships, maybe I should play with those... but this seems like a good quick solution to starship raids. i tried playing with spiders and they really didn't do anything to the mad bomber ships. Annoying!