Although the X-Men's Magneto is the undisputed mutant Master of Magnetism, vibranium is no ordinary metal. As the chief natural resource of Wakanda, the vibration-absorbing metal imbues countless fantastical inventions while serving a wide variety of purposes. And all of this begs the question of whether Magneto is able to decisively control the unusual substance.
Magneto has a long and complicated history with the magical metals of Marvel, and although vibranium is not magical, it is alien in origin, which might explain some of the mutant's unusual interactions with the powerful metal.
Magneto's powers allow him to command fictional metals as well as real ones, and he has demonstrated a mastery of adamantium -- the metal that coats Wolverine's bones -- and uru -- the material that makes up Thor's hammer -- as complete as any item on the periodic table. He famously liquified the adamantium of Wolverine's bones as he pulled it from his body and has deflected and redirected Thor's mystical uru hammer Mjolnir. However, when it comes to the mysterious metal of Wakanda, he has a decidedly inconsistent history. Vibranium has proven to be something of a challenge for Magneto to manipulate, at least at times.
One argument for Magneto not being able to fully control vibranium is posed in Christopher Priest, Sal Velluto, and Bob Almond's Black Panther #48, where Magneto faces off against the King of Wakanda. After taking a punch, Magneto states that the vibranium weave in Black Panther's costume protects the King from the mutant's magnetic influence, opting instead to pull metal from the surrounding room in an effort to entrap T'Challa.
What's curious about this instance is how easily Magneto manipulates vibranium in other instances. He never had any difficulty moving Captain America's partially vibranium shield, although it's nature means that there were other metals present in the shield that Magneto affected instead. The most compelling evidence for the mutant's ability to affect vibranium comes in Jonathan Hickman and Leinil Francis Yu's 2019 X-Men #1 in which Magneto faces a vibranium door and completely rips it asunder. This seems to settle the debate but also begs the question of why Magneto's powers didn't work against T'Challa in Wakanda.
The explanation may rest in the Panther's ability to disrupt Magneto's abilities. Magneto remarks on just how prepared Black Panther is, and given that Wakandan technology is advanced enough to be able to counter Magneto (much in the same way Iron Man proved capable of doing so in AVX #1) then there may simply be a mechanical disrupting agent rather than a material one.
It is not so much that Magneto cannot affect vibranium, but that the metal's vibratory nature and energy-absorption components can be harnessed in such a way that the Master of Magnetism meets his match. On its own, as proven in X-Men, Magneto retains his title as the master of all metals, including the mysterious vibranium.