Yesterday I encountered two somewhat annoying little bugs: I was allied with one AI and had just finished off the other AIs when I selected "keep playing" to finally deal with my ally. For some reason this did not cause his orbital structures to become target for my fleet-AI - my ships automatically killed the enemy's ships and reduced his planets to ashes but they ignored his structures. Even when I ordered them to kill the structures they repeatedly "forgot" their orders.
Additionally, after I had killed the last of his colonies through superior culture, his portrait remained intact. I searched the still uncolonized asteroids and planets for more than 15 minutes for a final colony until I realized that he was truely dead.