Like stuttering itself, the physical movements get reinforced by psychological conditioning. I've found that deliberately preventing myself from making those movements improves my fluency, and eventually gives me less to have to think about when I do stutter. I personally tend to tighten up and drive my foot into my chair and such, and it's both mentally and physically helpful to relax my muscles instead, even though they're not the ones used for speaking. You have to be very vigilant but it's possible to unlearn the secondary behaviors.