If, as you propose, sapient creatures speciate based on dominating their ecological niche, why would they see each other as competitors? To give contrast from natural world, ants war against other ants (and termites) - but only those ants which happen to be of similar size and eating the same food. Small ants and big ants co-exist comfortably because they are not each other's direct competitors.
Approached from a different angle, the advantage required to carry out complete, intentional genocide is vast. The simplest explanation tends to be that neither side is capable of exterminating the other. The second simplest is that the other side is trying hard, but you're working to stop them - that's what the fight against forces of evil genuinely is in many settings.