I was getting same issue with my carbon Moritaka. When cutting onion or something similarly reactive I was getting rust on the food as the knife started to rust immediately. What I do now is that I am wiping the blade with cloth very frequently so I it does not start rusting.
As I already asked in some other post:
Can any profi chef explain are Aogami/Shirogami knives are really used in profi kitchens? And how (constant wiping?)?
I really want to know how this is dealt with by profies.