Generally Pella and Andersen doors are meant to be installed before your flooring. If the doors are installed and then you add flooring your will take away 3/4-1.25" of the sill height. If the doors are installed in a kitchen with vinyl flooring then the sills stick up and create a tripping hazard. The doors are made to clear your "average" flooring (carpet, hardwood or tile with backer board), and in some cases they will clear a thick welcome mat.
Did your installers place a board under the door prior to the installation? If so, see if they can remove the board and lower the door by 3/4".