Here's a good article by the Athletic about it (paywalled though.)

Short version, fifteen players (mostly from Barcelona) protested against unprofessional treatment from Vilda and his coaching staff, and insufficient resources and backing from the federation. They requested not to be called up to the national team. Federation supported Vilda fully but later offered a compromise on certain issues, which is why some of the fifteen later returned for the World Cup. However, Spain are still missing key players who are continuing the boycott, most notably Mapi León.

I'm inclined to to believe the players on this, you don't have fifteen players refuse to play for their national team (with public support from another three, including Alexia Putellas) without having some serious problems.