The disappearing stone knife when you try to craft it is linked to the current animation bug (i.e the same as splints/skinning animals).
If you take the stone to hands, then F11 to start the suicide animation, then craft the knife while the animation of bringing fingers to head. This method crafts a knife everytime, if you don't do it this way then there is a good chance you get a message saying you crafted knife but it's no where to be seen.