MIB only knows about the numbers on the wall. He named all of the remaining people. HOWEVER, Jacob also touched Kate when she was a child. Kate does not have a number. MIB doesn't know this so he won't care about her. Kate is going to be the one that fixes and re balances the island. Also she is escaped from the Temple so she is wandering the island alone now. She might also be the one who kills MIB.