Hi Sweeney,
I assume you are burnishing after applying stain. First, make sure your burnisher is highly polished. Second, wipe it occasionally while burnishing to remove residue that will build up on it and cause it to drag. Finally, I have encountered the same thing you describe. For those spots, I clean the burnisher, lighten up the pressure and rub a little more quickly until they smooth out. The purpose of burnishing is to compress the wood fibers making a smooth surface and it also speeds up the process of building up the finish afterward. It is also important that the stain is completely dry.
dave