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It happened, like mid 90's in either Uncanny X-Men or Wolverine's own comic. Magneto finally just said F it and tore the adamantium out of him through his skin, I don't remember how they resolved the story. They found out after that he had bone claws inside of the metal, stopped following it shortly after, it's been a long time.
Thanks for the insight to the comic books (which I do not read)...!
Honestly, when you consider the magnitude and importance of the film series, and the fact that these are two of the most primary characters, this is likely one of the most egregious plot holes imaginable. If the two characters are on the opposite sides of good and evil, why wouldn't Magneto render Wolverine into a Human Pretzel from the get go?
My (limited) understanding of the adamantium is that though it can cut through pretty much anything else in the world, Magneto can still bend it, and once bent, Wolverine would not be able to bend it back. So again, at any given moment, Magneto could tie Wolverine into a bow-tie.
And just imagine that in the fictional X-Men world. Wolverine can heal, yes. But he also feels the pain of his injuries. Imagine the pulverization of his human bones as the admantium is bent into grotesque curving shapes. Every bone effected would experience hundreds of breaks and fractures. The bones would basically shatter.
THEN...
They would heal... They would heal back into whatever shape or curve Magneto has bent them. And again, Wolverine would then be the unrecoverable Human Pretzel.
For me personally, my extension of disbelief, (or powers of rationalization), allow me to believe that at the core, Magneto has a respect and a fondness (even an awe) of Wolverine's endo-skeleton, and for that reason alone, exercises a degree of "fair play".
Also, its fairly well communicated that Magneto is not truly evil. He has a specific cause, and is uniquely motivated to achieve his goals. Beyond that, though, he is not an entirely evil entity.
