I think I've been able to figure out part of this. In my current game, I've been going in with an Armored and a Cursed golem to AI systems, blowing up everything but the Command, warp gate, and wormhole guardians, and building research stations to gain some extra knowledge.
Normally, the cursed golem destroys all the zombies that spawn. However, cloaked zombies that spawn do not attack the golem or the research stations. Even upon leaving the system, these cloaked units never leave the system, even though "zombie" AI units are supposed to be aggressive.
In the game where the carriers went crazy, the AI had several cloaked unit types, which had built up in several systems after I harvested knowledge there.
Even then, I don't think there were enough zombies in that game to cause a sudden 150,000 unit threat level. Anyone got a clue what happened? Or should I make a bug report on Mantis?