The warning "Ignoring extra legend entries" happens if you call legend() with more names than there are lines in your axes. In this case, it is related to your use of "hold on".
Before "hold on" is called, each call to plot() deletes any previous line(s), so when you call "hold on", only the last line plotted (if any) exists and is "held onto". So when you plot three lines without having hold on and then call legend() with three names, legend only knows about the last line (since that's the only one that exists), so it gives you the warning because you gave it three names for one line.
The solution is to call hold on right after (or right before) the first line is plotted in each figure (instead of calling hold on after multiple lines are plotted). And also, when you change which lines are plotted (e.g., by commenting out the plot command) you should also change the corresponding names you send to legend().
% This is ok:
figure();
hold on
plot(1:10);
plot(2:20);
legend('a','b');
% This is also ok:
figure();
plot(1:10);
hold on
plot(2:20);
legend('a','b');
% This gives the warning:
figure();
plot(1:10); % you will not see the line shown right below here if you run this ...
plot(2:20); % ... because this deletes the previous plotted line
hold on % holds just the last line
legend('a','b'); % note that the 2nd line (2:20) is now called 'a' in the legend
