This issue is due to the Order Independent Transparency method used by MATLAB called "Depth Peeling." Unfortunately, there are no existing workarounds.
Changing to "opengl" setting to "hardwarebasic" gives a slightly better result, as this triggers the transparency to use an "object sort" method (Typically this is worse than any Order Independent Transparency method). Or you may use the "painters" renderer for the figures created by executing the following:
>> set(gcf,'Renderer','painters');
Our development team is looking into addressing this issue and it will be considered for a future release of MATLAB.
Best Answer