You might try using the painters Renderer. See below for a comparison of those three cases with painters vs the default OpenGL Renderer.
figure('Renderer','OpenGL')
fill3([0 1 1 0],[0 0 1 1],[0 0 0 0],'b')
hold on
plot3([0; 0],[0; 0],[0; 1],'color','#D95319','LineWidth',1.5)
figure('Renderer','Painters')
fill3([0 1 1 0],[0 0 1 1],[0 0 0 0],'b')
hold on
plot3([0; 0],[0; 0],[0; 1],'color','#D95319','LineWidth',1.5)
figure('Renderer','OpenGL')
patch([0 1 1 0],[0 0 1 1],'b','Facealpha',.5)
view([-37.5 30])
line([0; 0],[0; 0],[0; 1],'color','#D95319','LineWidth',1.5)
figure('Renderer','painters')
patch([0 1 1 0],[0 0 1 1],'b','Facealpha',.5)
view([-37.5 30])
line([0; 0],[0; 0],[0; 1],'color','#D95319','LineWidth',1.5)
figure('Renderer','OpenGL')
fill3([0 1 1 0],[0 0 1 1],[0 0 0 0],'b','Facealpha',.5)
hold on
plot3([0; 0],[0; 0],[0; 1],'color','#D95319','LineWidth',1.5)
figure('Renderer','painters')
fill3([0 1 1 0],[0 0 1 1],[0 0 0 0],'b','Facealpha',.5)
hold on
plot3([0; 0],[0; 0],[0; 1],'color','#D95319','LineWidth',1.5)
