Maybe it's an aliasing/subsampling issue. You can try making the lines thicker by setting the 'LineWidth' property:
load penny;
contour(flipud(P), 'LineWidth', 3);
axis square;
or maybe with your large dataset some contours are so close together that they are combining to make new colors. You can try to increase your increment/step size to make fewer contours that don't bump into each other.
