This bug happens for me as well:
Pump in a basin of water
Pipe from pump to inlet of filter
Purple outlet of filter goes to vent A
White outlet of filter goes to vent B
Configure filter to "contaminated water"
Result:
1/3 as much water exits B as enters the filter
Nothing exits A
I think I saw this happening with regular water as well. The conditions were:
Several algae farms freshly constructed
In a flat area that was slightly flooded with dripwater
Near a basin
The dupes were trying to pick water off the floor and feed it to the algae, but not making progress. The problem cleared up after save/restart/load.
Do you have a game pad plugged in? I haven't tried it with ONI but I've noticed that can happen with other games (X-COM 2) simply due to having a joystick plugged in.
Actually I think what might be happening is that they're trying to suck up the contaminated water, but there is no "contaminated bottled water", so they end up carrying nothing.
Sometimes my duplicants try to water algae farms with nearby contaminated water. The contaminated water immediately spills off the algae farm into the pit that the dupes got it from, with the result that they appear to get stuck in a loop of continually sucking up and spraying water to no effect.
I'll try to attach a video of this happening.
bugreport_contamwater.mp4