looked into the save and found it. You were nearly right. It is indeed because you are playing against a golemite. Everytime you trigger an enemy golem into attacking you (threat), it will appear as a warning as long as it's not on your planets yet. Your first warning wasn't a single bomber. It was most likely a golem that went on alert and wanted to attack you (which got destroyed by your defenses/fleet without you noticing it I assume).
Retreat the cursed golem on Yarco. Move all the ships and the golem to another planet, and you'll notice that the enemy regenerator golem your cursed golem was attacking will enter your planet (along with a bunch of other ships) and the warning disappears.
I'm not sure whether golemite spawns golems or not. I don't think so. I think all golems he has are already there when the galaxy is generated.
Did you just have a CPA? if not, may I suggest you kill all the big piles of threat? it's massive.
Good luck with your game, it looks quite interesting. You're gonna love that Raid Engine on one of the AI homeworlds ^^
EDIT: damn, got ninja'd