I was able to reproduce your problem:
x = [zeros(1,10); 1:10]; % Simulate Data
x = x(:); % Simulate Data
y = [zeros(1, 10); rand(1, 10)]; % Simulate Data
y = y(:); % Simulate Data
figure(1)
plot(x, y) % Reproduces Problem
figure(2)
plot(x(x ~= 0), y(y ~= 0)) % Fixes Problem
The solution is to take the non-zero values in both the x and y vectors, as I do in figure(2). That should give you the plot you want.
