The cube in the center doesn’t exist
But it is not one of the cubes that need to go to their correct locations. The center cube is not moved by any operation on the cube; it is always in its correct location.
(At least, that's true of the 26 outer cubes. You can't get them all into place without simultaneously aligning them correctly. I don't actually know if correct alignment of the center cube is also required, but it'd be my first guess.)
Nobody believes there are invisible cubes outside the Rubik's cube. That's not the same logic; that's you trying and failing to imagine a problem with the idea that cutting a cube into three parts along each of its three axes will generate a hidden central subcube.