Well, my thinking is "mutants" are an offshoot of the Inhumans. Like they have a "tainted" version of the Inhuman gene. Sort of like pure-breds and what not. You can have a pure breed horse (read pure blood Inhuman), and have that horse breed with a donkey (read human) and come out with a mule (read mutant). It has the horse's gene (Inhuman), but isn't a pure Inhuman.
This way, Marvel can say, "The Marvel Universe doesn't have mutants. They're an off shoot of Inhumans. Screw you FOX Studios!"