My son I sbuilding a new home and the contractor is not planning on installing a fresh air system. I am concerned about this since my son has allergies. Shouldn't a fresh air system be installed either in the HVAC or as a stand alone

Well if the contractor isn't planning on it, tell him that one is needed, its your decision what does into the house.. well your son's decision but you get me
Just tell him and its not like the contractor will say no is it?

Are you talking of an ERV? If so they intoduce fresh outside air, which is much healthier than most indoor air, and these units have there own filtration.