The ellipses are semi-transparent, so if some of them are drawn on top of each other the resulting color is brighter.

The answer is right beneath the code...

The dots are drawn with a low alpha (40/255 or about 16%), so when numbers are picked more than once, they get brighter.

So apparantly it's not just one circle per location, but more (depending on the number distribution) resulting in different shades when a transparent base fill is used.

ahhhh. duh, I see now. There should only be the same number of circles as there are original numbers?