It looks like you may be calling plot with x data that is not sorted. Compare plotting a sine curve with sorted data:
x = 0:360;
y = sind(x);
plot(x, y)
with the same call but the x data shuffled.
xs = x(randperm(numel(x)));
ys = sind(xs);
figure
plot(xs, ys)
You can see the general shape of the sine curve, but there are points that have very different x values that are connected with one another. Try calling sort on your x data (and using the second output to reorder the y data if it's already been computed) before calling plot.
[xs2, indices] = sort(xs);
ys2 = ys(indices); % Sort ys in the same order as xs was sorted
figure
plot(xs2, ys2)
