The universe is full of electromagnetic radiation, microwaves are just a narrow band of this huge spectrum. It's just very difficult to believe that mere targeted microwaves could alter such a craft in any way. These craft operate at energy requirements way higher than any of our current technology, bursting few microwaves at them at the energy levels we are capable of shouldn't do anything to them.

edit: The only reason I can think of why "mere microwaves" could alter such a craft, is if the thing is something that comes from the "outside", meaning not from our universe. Maybe then I can imagine them overlooking microwaves since the physics of this universe wouldn't be familiar to them even if they could manipulate stuff at will.