Delta printer distortion
i bet your towers are not standing straight (vertical) or 
your bed is not clearly horizontal

i've recreated your picture with some assumptions (for example that your SW calculates properly and your steppers and motors act well)

take a look here


if you deliver your printer dimensions 


tower height (from the base)
tower distance from the center
bed distance (height) from the base


i can calculate what is inclination angle on all towers but i suppose it's not really important

the important thing is to set them straight ;)

we can see from the picture that towerA is the most inclined to the center or
the bed highest point is next to towerA
(and i bet one of those or both cause the issue)

EDIT

i've made some calculations based on imagined assuptions of the tower height
here are details

    towerH | inclination
-----------+----------------
    300mm  | 0.11deg
    400mm  | 0.08deg
    500mm  | 0.06deg


seems to be quite small but in fact your differences in dimensions are also small

inclination of towerB is bigger as there is bigger difference in dimensions
so maybe the issue is more in bed "horizontality"

would be good if you would check and measure these params

EDIT2

here goes the explanation why bed inclination causes dimension distortion



of course it's exaggerated but it's just to show the issue