You can use Xdata and Ydata for this:
y = [2 2 3; 2 5 6; 2 8 9; 2 11 12];
h=bar(y);
% getting xdata and ydata from second bar in each group
xdata= get (h(2),'XData');
ydata= get (h(2),'YData');
% plot a * on second bar from second group
hold on;
offset=0.25;
plot(xdata(2),ydata(2)+offset,'-*');

If you want to mark the panel in the center of the group, this method works, but if you want to mark, for example, the first of one group, you must adjust the position * with the offset value on the x axis.
, :
y = [2 2 3; 2 5 6; 2 8 9; 2 11 12];
h=bar(y);
% getting xdata and ydata from second bar in each group
xdata= get (h(3),'XData');
ydata= get (h(3),'YData');
% plot a * on second bar from second group
hold on;
offset=0.25;
xoffset = 0.23; % manual set of get from properties of bar handle
plot(xdata(2)+xoffset,ydata(2)+offset,'-*');
