I discovered this with Hyperion Logistics, but I think it also applies to other super projects (Capitals, for instance).
If you build a Hyperion Logistics, then successfully invade an alien planet that's also building the Logistics, it doesn't remove itself from your newly conquered build-queue. If you let it complete, you now have two Hyperion Logistics with cumulative effects.
Also, since the AI hasn't finished his he'll build another one on some other planet. So between the two of you there's now three of the things.