Nanobots, or nano machines, are typically what we think of when it comes to nanotechnology. That's not the whole field, but those of us familiar with science fiction generally know the usual tropes involved. They are tiny automatons that can, depending on the setting, deliver pathogens to a target, or eat away at an enemy like termites. This also connects to grey goo scenarios. I found a few papers that suggest delivering pathogens would be most effective, being able to sneak through protective gear, but I couldn't find too much on my cursory evaluations.

I'm currently trying to write a story in a setting where nanobots are a challenge, and I want to figure out not only how to defeat them, but also what their natural flaws would be.

What would be the flaws with such a technology? My first assumption is they would be nowhere near as effective as they are claimed to be, simply because few weapons ever are. Energy demands are a major problem, for one, as is the issue of how you develop manipulators and other systems to work on that scale.

Say you have the perfect nanobot though. You can swarm an enemy. What would be the other flaws?

My instincts tell me they would have the same problems as biological and chemical warfare. While programmable, they would be too unpredictable, vulnerable to the wind, corruption from any number of subjects, and a unique challenge, they wouldn't be able to communicate very well.

So what would be the other flaws?