Player A cast Cannibalize that targets Creature B1 and Creature B2. Both creatures under control player B. Player B cast in response Feat of Resistance targets Creature B1. On resolution he choose black.
What happens on resolution of Cannibalize?

Player B has chosen….poorly.

The choice Player B is making is “which creature will get exiled by Cannibalize”. The chosen creature gets exiled, and the other target gets the counters. However, since the other target has protection from black, it can't be affected by Cannibalize. When Player B makes a choice of which creature to exile, they have to pick the remaining legal target - the creature without protection from black. That creature gets exiled. Since the creature with protection was not a legal target for the spell when it went to resolve, it can't be affected by the resolving Cannibalize, so it will not get counters from Cannibalize.

Nathan Long
Magic Rules NetRep