Emulator

I noticed this issue while researching how this game's bloom is rendered. Metroid Prime 3 has strange color splotches on environments with bloom. While the splotches do exist on console, they seem to be the wrong color in Dolphin.

Console:
http://i.imgur.com/GBNBlXo.png
http://i.imgur.com/Q8u1TFY.png

Dolphin:
http://i.imgur.com/53URpKz.jpg
http://i.imgur.com/LMPw0aq.png

They're introduced during the process of rendering bloom. Here is an example frame.

http://i.imgur.com/GQy8gxz.png

Notice all the red splotches - that's the issue we're talking about. This is what that frame looks like after the initial scene render at 640x528, before the bloom is applied:

http://i.imgur.com/gXahbQF.png
EFB alpha channel: http://i.imgur.com/DyrgKmQ.png (these are the game's bloom texture maps)

The next step of the process involves taking the EFB texture, downscaling it to 320x224, and alpha blending it on black. This is where the splotches are introduced. This is what the frame looks like after the downscaling:

http://i.imgur.com/7NrgfKD.png

With the contrast turned up so you can see what's going on:

http://i.imgur.com/lEBQ8v5.png

The bloom is rendered with this texture, which is where the splotching comes from.

That's about all I know about the cause of this issue.