Are you certain that all three Spire Civilian Leaders remain among the living? The AI considers them to be valid targets (and according to the patch notes, they have the same priority as things like the Advanced Factory, so they should be valid targets for exo-waves and aren't likely to survive long if they aren't covered by forcefields or other defenses when AI forces hit the planet they are on) once you've taken control of the planet, and I find that I frequently lose mine if I don't make an effort to protect them with forcefields and enough defenses to repel a wave, or at least delay it until I can get a response fleet into the system to clean up. They're especially hard to keep alive if they're at a border or isolated world, or if the AI makes significant use of fleet ships or starships which ignore forcefields, or which can deal splash damage to units protected by forcefields.