Actually, they use the main engines for orbital braking, I believe.
To me it looks like the nozzles on the OMS (Orbital Maneuvering System), which they use for attitude adjustment while in orbit, which are quite small.
The main nozzle is quite large, not a lot smaller than the main engines, but note the many dinky little nozzles near it (just dots on the large photo, shaded pink in the drawing), they look about the size of the one in the debris photo (which is obviously small, given the size comparison of the pine needles near it).