I would guess it comes down to ideology. Humanists are opposed to mutants, whereas Spartans strike me as super isolationist, so probably opposed to everyone that isn't a Spartan.
Not for me to decide, of course, but I could see the Spartans grudgingly accepting a mutant if they lived up to the Spartan lifestyle well enough.
It might be sensible for them to work together, but even in the real world, that's seldom enough.