There are several types of components that require surface mounting on PCBs. By far the most common are things like resistors & capacitors that are machine placeable. But others, like BGAs and through-hole components, often require hand placement because they require hand soldering and can't go through a wave solder machine. Additional possible complications are boards with components placed on both sides, or multi-layer boards with non-standard solder. Finally, Debug/Repair stations are always manual.
Source: Masters in operations research and 15 years experience writing factory control software for one of Foxconn's direct competitors & largest trading partners.