Guardians of the Galaxy director James Gunn has explained the shared movie rights between Marvel and Fox, specifically how the Skrulls can appear in Captain Marvel.
Much like Quicksilver and the Scarlet Witch, the Skrulls are licensed to both Marvel and Fox for specific uses.
Fans were both shocked and delighted to learn that the Skrull race will be the primary antagonists in the upcoming solo movie for Carol Danvers.
Many had assumed that the Skrulls movie rights were at Fox due to them being Fantastic Four villains; this was believed by many to be the reason that the Chitauri were the alien race featured in The Avengers.