Have you had your computer crash to the desktop when a planet flips? This seems to be connected to that bug. I would speculate that the computer has established the rally point earlier and continues to use it after the planet flips just as it did before the defection. Of course, the ships cannot enter the planet's orbit anymore, and they get stuck instead.

The AI wasnt rallying ships/fleets to the planet prior to flipping. And if you flip a number of planets you sometimes get multiple rally points.

Yeah, it does make it easy to sucker punch the AI, they can have as much as half their entire offensive ships at 2-3 of my planets, and normally they dont sort into fleets very well, alot of single warships. Makes for a very easy takedown.

In one game, the Arceans kept sending freighters to my homeworld and just leaving them there, because they had already maxed out their number of trade routes (that's the only possible explanation, anyway). It got so annoying--having several freighters clogging up my space for no reason--that I started buying them all up, and then used them to establish my own trade routes, or upgraded them to constructors. They never did stop building freighters and sending them over, either.

Hopefully the 1.3 update will fix up a lot of those weird behaviors.