It's not perfect, unfortunately. I'm not privy to the internal workings of the program, but I've quite often had to manually fill basins, even after running Fill Basins. I'm not sure as to why, but I suspect that it can only fill basins to the resoluion of the map, but it's easy to work or zoom in past that limit, and therefore run into potholes that weren't filled in, because it couldn't see them.