Maybe, while you are petting him, you found his weak spot. I find it on my dogs all the time, like on my Shih Tzu, her's is on the parting on her head. I reach down, touch her at that part in her head, and she shakes her head, and when I do it enough, she bends down and rubs her head against the floor. SO CUTE!
its just a natural response and action of all rabbits including those is the wild, no hidden meaning and doesn't mean they are going to pounce or are weird, I have never seen a rabbit that doesn't do this