Corrected entry: Kitty phases a toothbrush into Beast and leaves it there. he should have noticed something that size of a toothbrush poking through his internal organs - and should have suffered some sort of damage from it even when it was phased out.
Corrected entry: Where did Bobby get his X-Men uniform from? He wasn't wearing it under his clothes. And if the mansion was demolished, he had no way of getting it. Yet he appeared with it on.
Correction: He isn't wearing it until they steal the x-copter back. There were spare uniforms onboard, Cyclops changed at the same moment.
Correction: Not unless Beast is a machine. Kitty's phased objects can stay phased for a long time, at least long enough for it to slip back out of him. The only damage is that they blow up machines.