I am not a medical professional, but I don't recall any established biomedical reference stating that chlorine dioxide occurs naturally in the body.
Maybe if you were struck by lightning...
To take this to the next step, it is one thing to theorize that something occurs, and quite another to actually measure it. There are no instruments available that can measure chlorine dioxide inside the body. They have looked at this a lot for use during industrial accidents. What they found was the chlorine dioxide is so unstable that it doesn't last for any length of time inside the body. However, the chlorite disinfection by product does linger, and it can be measured. Since the chlorite free radical damages the body at higher concentrations, those levels are monitored when people have been exposed to high concentrations of chlorine dioxide.
I don't believe chlorite occurs naturally in the body either.