Bigtime, that foaming bore cleaner is a nitro powder solvent. You should really be using a black powder/substitute cleaner. Thompson Center has a product called T-17 that is a good cleaner for BP and its subs. Another word of advice, ditch the wire brush for your cleaning and use a nylon brush. Montana Extreme has a brush for just about any bore size up to .50 cal.
Let us know if these spots turn out to be rust. I doubt it with you using the gun oil after cleaning.