Is the loop still telling the figure to plot even if there isn't any data recorded? You have a few ways around it:
The first one basically tells the legend to put an "empty" headline for the second item (if nothing was plotted)
legend('item1', '', 'item3')
You can also only tell MATLAB to plot only when there is data with
if isempty(your_matrix)~=1
plot(x,y)
end
There are also other ways which you can tell the legend to ignore some entries. You can also enter the plot tools (in the top menu of figure) and do it without code.
