Its as obvious as the eyes on your face that the eye sockets in the skull would not have evolved through any kind of natural selection and random mutation but rather had to be the result of a planned design.
But the skull of this early ancestor was not a shrunken version of our own skull. It was not necessary for everything to evolve at once. For an example look at the sharks skull. There is a brain case, which in sharks is made of cartilage just like the rest of the skeleton. There is no eye sockets as such, with the jaws being a completely separate section. It would be later in our evolution ossification occurred and the various elements which make up our skull became one contiguous unit, and by that point the eyes would already be developed.
It's important to remember, as others have pointed out, that our skeleton is not a preordained blueprint in our genes. During development the cells act like a colony reacting to the local environment, in this case other cells. So nerve cells in the brain are not going to grow through the cartilage that will later become the skull, just as cartilage for the skull is not going to be laid down through the eyes.
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