Solution from Chrysanthos Placotas in mathworks.
" When you make the object transparent, it means that the objects behind it need to come on the "front". When the object comes on the front, its edges are traversing it, but the color does not change since it is opaque. "
Instead of making transparent, he suggests making same colour as background
set(get(childHandle(3),'Children'),'FaceColor',[0,0.3922,0.6078],'EdgeColor',[0,0.3922,0.6078]);