I was actually at WDW when they were filming and we filmed them while we were at Indiana Jones. LOVE those two episodes to death.
Anyways, as a smaller scale fish tank hobbiest... Not saying this is the case, but when I maintain the tanks, what can happen is when you are siphoning the bottom (Sand, gravel, ect) it stirs everything up into the water and doesn't get all siphoned out. This leaves you with very cloudy water. Picture not being able to see your fish unless they are up to the glass kind of cloudy. But luckily this problem only lasts about a day as the stuff in the water settles again. Another issue is when you replace the water (This happens even when you start a new fresh tank) there are so many tiny bubbles that the tank looks cloudy from that. Combine the two and you would be better off going to Turtle Talk than to see a wall of cloudiness. And considering that The Seas is on a large scale, they must not do siphoning of the bottom regularly. But as far as water goes, the larger the tank, the easier it is to maintain water quality. If it was indeed an outbreak in the water itself, there are treatments that change the water all types of colors. One I have used often is one that turns the water a florescent greenish yellow. It makes the tank look like it has a power plant leak. But I could probably say safely that it is not the case because these chemicals need to run for days without filtration and need to be added over that time.