Most medium-burning powders like those often used in the .45/70 and other large-volume, straight-sided cases, will evidence incomplete burning when the pressures are kept low enough for use in some of the older rifles, like the trapdoor Springfield. I used to have an Argentine Remington rolling block in .43 Spanish. My load used the Lyman cast 439186 bullet and 45 grains of IMR 4895 for low pressures. Although this load was pretty accurate and gave a MV of 1400 FPS, it left A LOT OF UNBURNED/PARTIALLY BURNED POWDER GRAINS IN THE BORE. Seems like what you are seeing is a similar thing. The slower the powder, the worse it is. But as long as your velocity & accuracy are acceptable, it is no big deal.