Very minor genetic differences can create major physical differences.
It's not too surprising for multiple sentient species to evolve on the same planet. I don't buy the nihilistic 'They will necessarily destroy each other' argument. The most likely scenario where multiple sentient species evolve on the same planet is, right when they start to become sentient they become physically separated, then when they find each other again there aren't any major technological differences so one is not capable of just dominating the other and they are forced to get along.
In the Xindi case, this seems likely, because all five of them occupy different environmental niches where they do not compete for the same resources.