Did you make sure to get all the foam out of the bores after you treated them? Did you run a patch of gun oil down after dry swabbing?

I don't use foam personally so can say for sure but it could be residue your seeing left behind.

Could betooling marks from rifling process or even pitting or damage caused by copper be left on the steel.

Do you clean from the muzzle or breech? Do you use a bore guide and coated rod?

Possible the scratches are from cleaning technique and tools. If a bolt action it should be cleaned breech to muzzle. You should use a bore guide to keep the rod centred and a 1 piece coated rod to eliminate the possibility of scratching via contact and flexing while in the bore.

Just a guess though, if you are sure you've removed the faom agent and coated the bore with oil you could take it to a gunsmith for their thoughts. Or maybe one of the forum members who aregunsmiths will chime in.