Yep, there will sometimes be stuff that just won't come out. Take it out and shoot it out. Worked great with my Turk Mauser, and my 1905 Tula M91. If you're going to store it for a while wherever you keep your gun for a prolonged period, like a couple months, oil the barrel up you might get some of that rust in the hard to clean spot creeping back up on you after while.
I have a Finn 91/30 this problem happened in. The bore was like new except for this one spot that had some rust from someone not cleaning it after shooting. The bore was also pretty dirty when I bought it. I cleaned for a long time, and finally put a few rounds through it. Just warmed the barrel up a little and pulled a bore snake through it with a patch of Hoppes at the time. Worked great, bore looked amazing. So I went and cleaned it up. I will periodically check the bores to make sure nothing is growing in them, and found a little bit of rust in that one spot. So I cleaned it out, and oiled it up.