Both the supply and return are restricted, not only by improperly sized ducts, but by poor workmanship. Your contractor will have to fix this properly or the system will be a headache forever.
This is not the equipment's fault. Any system would have problems installed in this manner. They are just not smart enough to tell you until it is too late, and something major fails or there is property damage.
The "unknown" is probably due to rapid fluctuations in the supply air pressure in the discharge plenum due to the poorly installed discharge plenum.