During my tenure in Browning's gunsmithing shop I did a lot of hot water bluing of Superposed shotgun barrels. We always wore new heavy duty rubber gloves and never touched the metal, we used Herter's Belgian Blue which I believe is still available from Brownell's. The blue solution was suspended in a small Pyrex dish in the hot water tank so it was hot and we applied it with a pad of roll cotton. The cotton pad was kept in the dish of blue and squeezed out dry to apply to the metal in long even strokes. The fine carding wheel was run at low RPM and a Crystolon wheel dressing stick was used to gently bend the ends of the wire over ever so slightly. In my experience areas like you speak of were often the result of technique with the wheel or not waiting long enough and carding fragile "young" blue. It took me a while to get the technique with the wheel down and even then there were some parts that would have patches like you experienced and would require a re-do.
