Unfortunately I can't go back and double check because I don't have a save, but I took time to clear every of the three planets completely, of every guard post and all straggling units, so unless counterattack posts are destroyed on destruction of the command post, I am quite certain I did not encounter any counterattack posts. I don't think I'd have missed or misclicked on a counterattack post either, because they look very distinctive. I think I've also seen this before in another game, but at that time it was only a 300-wave and I didn't think much of it, I just thought it was a new feature added in (rare strikes from deep space).
I wish there was a way to test this, but I don't even know what would've caused this if this is a bug.