There are several problems with the Xindi. But also with evolution in Star Trek in general. It is deterministic, it produces abundant intelligent life, mostly humanoid.
But, what is the issue? That they are related? Or that they are evolved?
To their relation: Just from a statistical DNA view-> If they are from the same planet, the should have some 40-60% similarity. If we add the percentage of similarity that exist between advanced humanoids (the fact that different alien species are genetically compatible, think on all those hybrids) we could come up with a greater number.
If we take a look on the point that the Xindi evolved on the same planet:
Yes, their different environments could be the answer->
Xindi-Aquatics - sea
Xindi-Arboreals - ???
Xindi-Avians - ???
Xindi-Insectoids - ??? (rain forests, some place humid)
Xindi-Primates - ???
Xindi-Reptilians - warm regions
As most races in Star Trek have a small drive to expand, this could be similar in the Xindi and they did not have the opportunity to wipe each other in their Neanderthal stage, but only met each other in their Antiquity, when they were on equal footing.
We should also note that they did not have to have evolved, but could have been uplifted by some old race...