It seems like a concern but actually it isn't. As long as you get it out. I clean all my traditionals using the hot sopy water and very hot clean water rinse. Its amazing how quick the surface can rust. After my rinse, I swab the barrel with clean dry patches until this brown coloring doesn't show up on the patch. Then I run some dampened patches of #13 Black powder solvent down the bore and then dry. Final step is a patch with (Don't tell Cayugad) bore butter.