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A mental block, he's shown before he can control the powers of others but I highly doubt Charles has anything to do with why there's no more mutants.I think the biggest hint to what's happened is.. Charles. Them saying he can't control his powers is what I'm referring to.
If I had to guess, Charles unknowingly kills off most mutants and depowers the rest after having some kind of psychotic break or something. Wolverine still has his adamantium and claws (like in the episode of the 90s cartoon where they travel to the Savage Land to free Charles and Magneto from Sinister), but has severe pain retracting them (because no healing power) so he doesn't use them any longer, also his rapid aging is becayse of not having his mutant power any longer.
How would Professor X stop people from having their powers?
Logan even says something like let somebody else do it or others will show up so there probably still are some mutants left.