One of Magneto's biggest mistakes was almost inspiring an apocalypse brought on by an army of nanotech zombies. In the Ultimate Marvel universe, the X-Men are sent to the Savage Land to figure out why hundreds of Special Forces soldiers have suddenly disappeared during a mission pillaging the remains of Magneto's destroyed mutant citadel. What they find is that, among the rubble of this mutant haven, a technological entity has been secretly mutating and working on its plans to replace humanity with an amalgamated army of techno-organic zombies better suited for life in the 21st century.
In this parallel Marvel dimension which introduced readers to a modern world of characters not bound by years of continuity, the Savage Land citadel was the creation of Magneto and Charles Xavier to be a mutant utopia. When Charles and Erik split due to ideological differences, Charles' X-Men and the world became Magneto and his Brotherhood of Mutant Supremacy's enemy. The citadel was decimated by a massive Sentinel attack which killed many citizens and was later abandoned after Magneto's attack on the United States was foiled by the X-Men. In Ultimate X-Men #22, it was revealed the U.S. government sent in soldiers to investigate and pilfer the citadel's remains in hopes of finding anything unclaimed that could be repurposed or patented. When the communications failed and a hundred Special Forces soldiers went missing, Charles Xavier volunteered to send a team of his X-Men to investigate.
In Ultimate X-Men #22-24 by Mark Millar, Adam Kubert, and Kaare Andrews, Cyclops was forced to travel with his romantic rival Wolverine and their unknown stowaway Kitty Pryde to the Savage Land. Searching through the ruins, both mutants find some of the missing soldiers, now transformed into nanotech zombies whose attacks are no match for adamantium claws or optic blasts. The mutants learn these soldiers are only following orders, their leader happily revealing itself to be the supercomputer that once maintained the citadel. This brainchild of Xavier and Magneto was left abandoned after the Sentinel attack and was motivated by its "fathers" to evolve, growing strong enough to gain the ability to convert the corpses of slain mutants - and later the unwelcome soldiers - into an army that'd help it rebuild itself. Nearly complete, it announces its new goal of continuing to create a new species that would quickly replace both humans and mutants completely.
This new techno-mutant has some things in common with Astonishing X-Men's Danger, an artificial intelligence that manifested from the X-Men's Danger Room. Both were sophisticated AIs that evolved out of programs created and used by mutants. However, Danger was kept a secret by Charles Xavier so he could continue to train the X-Men and when Danger was free, she took revenge both on Xavier and the mutants he valued more than her and her freedom. This other entity was created by Xavier and Magneto but was forgotten when its sole purpose was abandoned where it was forced to evolve or die. After it created enough of an army to rebuild itself, it couldn't help but brag about its progress and plans for worldwide assimilation to a small audience of those it used to serve.
The pride of the AI-controlled machine seen in Ultimate X-Men quickly led to its demise as it was destroyed when Kitty Pryde accidentally phased through it. Although the X-Men would face Magneto soon thereafter, it is unlikely the mutant terrorist and supremacist ever learned how close a mutated machine of his own creation came to achieving his goal of destroying humanity.