While I am not 100% sure if it really is a bug or not, it seemed odd enough for me to ask about to make sure. To start with, this is the setting I have for it for the game it happened in.

Which from what it sounds like to me, the academy will stay on their home system unless players gift them other systems or something involving player or AI faction interaction. However, this is what I saw on turn 10 of a Nakalim playthrough on normal speed on normal difficulty.

Regulus is an academy system now somehow (and not even the only one at that) while Echius is their home system for that game. And 10 turns into normal speed on normal difficulty seems like it would be way too fast for the AI of any faction to assist them in any way. So unless there's something missing here that I'm not getting, this seems like a big bug for that given setting.

If it helps, I'm pretty sure I have the diagnostic for that game on hand that I can send upon request.