Originally posted by Q99
Because it can mess with his insides and such without having to try and break his outer shell.
Wrong. Wanda's hexes work on Ultron because it affects it's very own Molecular Arranger, regular magic has yet to prove to be useful against him.
HOWEVER, since Ultron doesn't understand magic I don't think we should assume his defenses would work against an experienced high level mage. Magic is not a weakness of Ultron per se though.