Why machines have energy efficiency less than 100%

Because of the conservation of energy.  You get out of a machine the energy that you put in in an ideal situation. (energy works like a piggy bank.  If you put in $1.00 you will never get out more than that).  Since machines have internal friction, losses due to heating, air resistance while rotating etc. some of the energy you put in is lost.  It is lost in compensating for these inefficiencies. The efficiency is the ratio of output to input.  Since output is less than input you have a number that is less than 1.