Each nonobyte (excuse if not correct term) is hackable, kind of like a digital webcam. Tony's hardware has been hacked before. What keeps each piece of nano technology from being taken over? Good cyber defense? Would this be a good business to be in?
The problem with most characters is they can be controlled by telepaths. The problem with most animals is they can be controlled by characters with animal-control powers. At least Stark can actively work to invent defenses for his tech. Most characters just are what they are, and are screwed if they run into something with an appropriate enslavement power.