Well, I know what you mean when you say the body has its own mind. As a doctor, I like to think of it as the Autonomic nervous system. And the reason we contradict our own reason is because of deeply ingrained thoughts that we are sometimes unaware of. 

I Have a friend that would only react to strenuous events after 2 or 3 weeks. I mean she would just start crying for no reason. She would find that she was reacting to something that happened 3 weeks ago after she sits down and does some self reflection. And that is just one of the many stories.

There has been a lot of debate on whether the body has a mind or not. It's the mind-body dualism theory. 
It's been on for a long time, and I still don't know which side to pitch my tent.