The behavior above is occurring due to how the coordinates are being extracted and plotted. In MATLAB, when you use get(gca, 'CurrentPoint'), it returns a 2x3 matrix, where each row is a point in the form [x, y, z]. The first row corresponds to the point in the axes plane, which is what you want for 2D plotting.
To resolve the issue, you should add the following lines after waitforbuttonpress. This ensures you are using the correct values from the matrix returned by get.
x = scale_start(1, 1);
y = scale_start(1, 2);
Also, plot the point using the correct x, y after hold on.
plot(x, y, '+r');
Here is a screenshot with the 'red +' being marked at the exact point where clicked and not just on a straight line:
