The character's origin story was altered by comparison to its Marvel Comics source material when she was introduced in Captain America: The Winter Soldier's post-credits scene and fully in Avengers: Age of Ultron. In the comics, Wanda Maximoff and her brother Pietro contain the mutant gene, the key characteristic of heroes and villains making up the X-Men characters. However, with Fox owning the cinematic rights to the X-Men characters and their traits, Disney was burdened with altering the story for the children of Magneto in order to use them.
With a deal with Fox and Disney looming, which would allow the Fox-owned characters to be rebooted or merged into the Marvel Cinematic Universe, a new book recapping the first 10 years of Marvel Studios is planting seeds for Scarlet Witch to be a mutant, all along.
"She may be called Scarlet Witch, but Wanda's powers aren't derived from the occult," the book reads (via ScreenRant). "Whether it altered her or merely unlocked something latent inside Wanda, the Infinity Stone on Loki's scepter bestowed incredible powers of the mind. Wanda's internal neuro-electric interface allows her to conjure blasts of red telekinetic energy. She can also use this energy to create barriers, levitate and move objects; to communicate and read thoughts by telepathy; and even to manipulate the minds of others."
While Marvel Studios might try to smooth over a hidden mutant gene having existed in Wanda all along, the notion of introducing her father is perplexing. A major driver for Wanda and Pietro in Avengers: Age of Ultron was their parents having been killed by Stark Industries weapons, fueling their desire to see Iron Man killed.
While the death of Maximoff parents was never shown on screen and fans know not to accept a character death in comic book movies until they see a body, such a reversal on the story might not sit well with some fans of the MCU's continuity. At the same time, they might be so happy to see the X-Men being introduced to the mix that it could be a forgivable retcon, of sorts.
Wanda Maximoff may or may not appear in the next Avengers movie, which is slated for release in May of 2019. In Avengers: Infinity War, the character was wiped from existence when Thanos snapped his fingers with a fully formed Infinity Gauntlet. This would mean both of Magneto's children are currently dead, so maybe the trio will be resurrected in some fashion for a very unexpected, X-Men heavy Phase 4?