The reason is that you are trying to create a plot with a single data point multiple times. So each time you plot there are not two points for the plot function to connect.
A simple change is to make y and x y(i) and x(i) then plot outside the for loops.
With Matlab you can probably throw out the for loops altogether with matrices:
figure
i = 1:102;
y = mean2(data.data_dic_save.strains(i).plot_exx_ref_formatted(87:151,83:151));
x = i*4;
plot(x,y)
