The way I understand it is when things like blocks or intake manifolds are cast, they are cast of molten metal poured into a mold. But something like an intake manifold with have two molds, one for the outside shape and one for the inside shape, then the metal poured in between. The inside mold would be the core. But if the two molds don't stay perfectly aligned through the whole process, you get what's called core shift, because the 'core' has shifted away from where it's supposed to be. I assume that happens because of the cooling process or just from the pouring of the metal.
Someone correct me if I'm wrong.