I'm not sure if I found a few bugs or if I just failed to pay attention and realize these things in the game, but it seems to me that the following happened:

1. It appeared that they (Sophons/Cravers) colonized systems without using a colonization ship. 

2. It appeared that they (Sophons) ignored a siege/guard of a system and escaped with a colonization ship.

Now it is completely possible that I simply missed these things happen or misunderstood somehow. Assuming that isn't the case, I guess these would be bugs?

I'll attach my save, maybe it will help: I don't understand what is happening.zip