I think there are other ways to get the eyes, you have one in the cauldron room in a jar and another in the lamp on the library. Try with those two.
im sure all you have to do is to go thru the same room again to get the knife? when the scene ends youll need to go inside the painting lady room again and get the black object
OR youre talking about the KNIFE itself not the black object, to get the knife you have to interact with the black object and ask sai to cut himself to get the knife