Why is the work output always less than the work input?

Because energy is wasted either in the form of heat energy or something else (like friction)

Because of energy loses. Energy is lost as heat or sound etc, the system is not 100% efficient. Also as work done = force * the distance the force is applied, because of the friction force, the actual force that is applied is reduced, thus the value for the work done (change in energy) becomes less.