Many of these colors that don't actually show up on the NES palette. For an easy example look at the blue/gray on the top middle and try to find it on the actual palette. Most if not all of the other colors are slightly off as well if you check the RGB values. Granted sometimes the colors can get a little off through conversion between different file types, but not by that much.


The NES only actually uses 3-color palettes + a background color they all have in common, usually black. All the other tiles have black in common but the sky uses 3 shades of blue... and white.
Now, even assuming it was planned to change the palettes to denote the above/below water parts of the stage there are still some issues. Look at the animated warning lights on the side, for example; white, orange, black (background) leaves 1 color (which is apparently being cycled). Making the lights different colors means that this sign actually has to take up half of the 4 tile pallets the Nes can show on screen at a time all by itself. If you look at the green (or recolored blue) tiles you'll notice that some use white and others have red for the lights, meaning that these also use 2 palettes. How does that leave room for the grayish pipes/ladders tiles or for the bluish backgrounds? Did you notice the spikes are using black with the sky blues, meaning it's yet another palette?
Actually knowing it's all the same guy explains why the MM#FC games make these sorts of errors all over the place if you look carefully. Take this screenshot from the beginning of MM8fc's Aqua Man stage:

How many tile palettes are being used here?
1) sky+water
2) stones
3) pink pipes
4) green pipes
5) grey pipes
6) orange pipes
Well that's a problem, because as I said the NES can only do 4 palettes of tiles at a time. And no, the grey/orange and pink/green pipes can't be using the same palettes because they each also use dark green/brown and white/light green for shading. Including black that would make a 5-color palette, again soemthing the NES can't do.
I think I've made my point. [/rant]