The cleaning does not drain the contaminated water, it simply disappears. Pure water arrives and is consumed, animation of the drain occurs, but contaminated water does not flow into the pipes.
Steps to Reproduce
I did nothing, just built the toilets and followed the movement of the water.
Status: Known Issue
We are aware of this issue and have it logged internally but either we do not have a fix ready yet or we are not planning on addressing the issue in the immediate future.