Print not completing filling in one direction

Rep rap i3, repitier using either cura or slic3r prusa edition. Any other details I can find out just ask. It does this for all my prints now.

because it happens in the same spot on all squares it appears to be an error in the design you need to print a regular cube and see. You should calibrate the extruder it could be under extrusion

Are the "square" holes the right size? Im trying to decide if the infill is short or the perimeter is wrong.
Is that one perimeter?
Can't be missing steps or it would get progressively worse.
Can't be retraction as it only happens at one end of a run.
Are the X and Y motors the same type and have the same step settings. Its almost like a position error on one axis but it doesn't happen on both infill and perimeter.