I had exactly the same mysterious experience. I posted this below yesterday.
With the release of the new beta I've decided to take the plunge and get to grips with this game.
Now, I started a game and well.. rage quit
I was playing on beginner on a small map and I had built 2 x cultural starbases, various consulates with the stacking bonus for adjacency in a single system. My borders were slowly pushing back the borders of the only AI I was playing with when suddenly, in the middle of my territory, a "strip" of AI influence appeared. This strip then proceeded to cause one of my primary worlds (filled with consulates) to become annexed.
The result was.. messy. The influence that system was providing essentially wiped out my entire territory. I even attempted to build another cultural starbase to prevent what I knew was coming...
I thought I was safe from this as my borders were pushing the AI's back...
Any ideas as to what on earth happened?
It makes no sense to me at all.