WARNING: The following contains spoilers for SWORD #1 by Al Ewing, Valerio Schiti, Marte Gracia & VC's Ariana Maher, on sale now.
Despite embracing all mutants as a part of the new Krakoa ideology, the X-Men still have plenty of enemies that they've come to hate over the years, including long-time Avenger Scarlet Witch for her role in the decimation of the mutant race. But it turns out that conflict comes with some serious repercussions.
The X-Men holding onto a grudge against Scarlet Witch has cost them a stronger partnership with the Kree/Skrull Alliance, presenting an unintended roadblock to the galactic expansion of Krakoan interests.
While touring the Peak, Magneto, the Quiet Council representative to the station, gets the chance to meet the diplomatic branch of the organization. Now run by his former Acylote Frenzy, Magneto also meets Paibok, a representative of the Kree/Skrull Alliance. The Skrull diplomat is set to serve as the galactic ambassador to the Peak. Paibok is very impressed with the Peak and the seemingly the mutants in general but admits there might be some problems bringing Emperor Hulking to the station. It turns out that Hulking has issues with the fact that Krakoa named Scarlet Witch more-or-less an enemy of the state and not just because she's an Avenger, but also Hulking's mother-in-law following their wedding during the events of "Empyre."
Paibok even mentions that Hulking considers it a "great shame" that the mutants don't think highly of Wanda which earns him a pointed glare from Magneto. Scarlet Witch has become something of an infamous figure on Krakoa, especially with her current status as a "fake mutant" who had been given her powers by the High Evolutionary. Mutant children even tell stories of her around the campfire as if she were a monster. In the aftermath of "House of M", the Scarlet Witch's fury with her father led her to remove the powers of roughly 90% of all mutants, leading to an extended period of increasing isolation and desperation from the remaining X-Men.
The act has left much of mutantkind furious with her, although there have been some hints of a few X-Men who would like to see her as a friend again, such as Beast and Magneto. To her credit, Scarlet Witch's acts have also weighed heavily on her in recent years, with the X-Men's involvement in "Empyre" being set off by Wanda attempting to resurrect the millions of mutants wiped out in the Genosha Massacre, only to accidentally bring them back as the undead. Despite even having worked with many X-Men during her time with the Uncanny Avengers, Krakoa is still wary of the Avenger, especially given her history with mutants.
Magneto and Scarlet Witch both seem fully aware of the chaos that Wanda has brought to the X-Men over the years, and the damage it had on the mutant community. But now, that continued antagonism could doom any future plans the X-Men have to ally themselves with the Kree/Skrull Alliance, which together can stand up as one of the galaxy's most powerful forces. However, this might also play a role in the eventual fall of the alliance, which was teased in the final moments of Empyre to involve the arrival of SWORD as last-second allies to an all-but-defeated and abandoned Hulking.
Perhaps something happens between then and now that changes his views on the Avengers and their relationship with the X-Men. But as for now, the Scarlet Witch is keeping Krakoa from expanding their influence, proving that she's a detriment to the growth of the X-Men, even when she doesn't mean to be.