It is normal for there to be a space at the back (hinge) of your PlanetBox Rover, Launch and Shuttle.  It is an intentional part of the design and allows the box to accommodate the Dipper(s).  The back of the PlanetBox does not need to be flush with the hinge and on the Rover, in particular, the rear right side (when looking at the back of the lunchbox) is slightly lifted.