You have to realize that in a stacked bar plot you really have 2 bar plot objects, not 3 like you seem to think. You can modify the two 'Facecolors', the first group of bars and the second group
A = [50 25; 5 5 ; 25 50];
h = barh(A,0.75,'stacked');
xlabel('Seconds');
set(gca,'yticklabel',{'Green','Yellow','Red'});
set(h(1),'Facecolor','yellow');
set(h(2),'Facecolor','red');
Or pass a vector
A = [50 25; 5 5 ; 25 50];
h = barh(A,0.75,'stacked');
xlabel('Seconds');
set(gca,'yticklabel',{'Green','Yellow','Red'});
set(h(1),'Facecolor',[0.5 0.5 0.5]);
set(h(2),'Facecolor',[1 1 1]);