Well, it didn't help that all the non-X-Men mutants rather clumsily were retconned to somehow NOT be mutants anymore, like Scarlet Witch, Quicksilver, Franklin Richards, and Squirrel Girl.
I don't blame anyone for raising an eyebrow that Marvel was so quick to boot out all these mutants that helped flesh out the Marvel universe beyond X-Men books, only to retcon an unaffiliated character into a mutant and immediately start putting her in X-Men books.