If you only have two layers, the first layer is colored blue, and the second layer is colored light blue, because that’s the first two colors in d3.scale.category20(). That’s a pretty bad choice – the layers are hard to distinguish because they’re the just the same hue with a different lightness/saturation, and light blue is also hard to see against white landmasses (once you’re zoomed out far enough that streets etc. are no longer visible), and almost invisible against the ocean, which is also light blue.

I’m not sure what the best solution to this is; perhaps using d3.scale.category10() if there’s ≤ 10 layers?