The work output of a machine is less than the work input what factor cause this

Total work energy on the input side is WE = Fs; where F is a force acting on a mass to push it s distance. This is the so-called work function. Let fs = we, which is the work energy (useful energy) attained as output when WE is input. 

From the conservation of energy WE = Fs = fs - kNs = Total Output energy. Net force f = F - kN where kN is friction force acting against the pushing (input) force F. In the real world, there is always friction at some level. That is kN > 0 always. 

Thus Fs = (F - kN)s; kNs = the energy lost to friction where k is the friction coefficient and N is the normal force on the surface(s) where the friction is generated. By definition, efficiency = fs/Fs = useful work/work input. Clearly fs = Fs - kN < Fs . Thus efficiency = fs/Fs < 1.00, which means output fs < Fs the input whenever kN > 0, which in the real world it always is. 

The short answer is...output is always less than input because of friction and, sometimes, other losses like wind drag (which is a form of friction anyway).

On the galapagos islands charles studied finches