A manifestation as in the presence of something, but not precisely that which I would classify as being wholly independent. For instance, if a source of the anomaly was located and extinguished, the manifestations of little girls or shadow figures would cease to be. You would not be seeing them everywhere you go.
A ghost is something wholly independent, acting of it's own will (for better or worse), or is confined to a predetermined area such as in a known haunting of a specific location. Ghosts must expend energy to act, or feed on the energy of others in order to gain the power to act, be it by absorbing the fear or anger of the living. Or by consuming the powers of other ghosts to grow stronger.