Well, by moving around I meant the map, not the grav well. So yeah, it basically sounds like what I described. The actual "AI" was dead, but the combat behavior for ships was still active - so the colonizer auto-cast, and his fleet engaged you in the grav well.
This is a weird byproduct I guess.. initially, you only had to destroy planets to win. They ninja-changed it to planets + colonizers, which opened this weird loophole. Definitely strange