Shadowcat's ability to phase through matter comes from the fact that her phasing power works by letting her atoms pass through the spaces between the atoms of another object. Because her atoms and the object's atoms never touch, she achieves the ability to quantum tunnel herself through that object. However, even though her atoms never touch, they do disrupt the electron field of other atoms. For machines, this causes the electron flow to destabilize, which in turn causes the machine to malfunction or explode.
