I think what has happened is that there may have been a colony ship station at a planet and when the planet flipped, the colony ship was ejected. We'll look into it.
Yes, that was the case (one colony and two transports). What is strange about this is that the AI then stops moving its ships altogether after this. Maybe it does not have any range afterwards as there are no planets to calculate it from?
This might be useful looking into as the scenario could also happen to the player. Otherwise it might be best to kick the player out in such cases
Please find the below save to check it out: https://www.dropbox.com/s/jg0hj4nibz51shz/Helvetia.GC3Sav?dl=0
The above save could also be useful to improve AI behavior as it displays a pretty competent AI as well as numerous others that fail to pose much of a threat to it although I have paid them all to wage war on the dominant player at the same time, have quite capable economy and enough distance from the enemy to build up