I guess Phantoms might count
Ben Affleck (aka the bomb yo) seemingly kills the Ancient Enemy, but it turns out to be alive at the very end
Species 1 and 2 end on sour notes. in the first one, while Sil and her child are destroyed, a rat eats some of their leftover DNA and becomes a hybrid as well. Species 2, they kill Patrick though Eve dies as well IIRC and her stomach swells with new spawn at the end