Spotted when having a small layer of water over polluted water to prevent it gassing, and the cistern begining to break. As the bottle emptier fills empties it adds the mass to the polluted water tiles as expected, but doesn't seem to want to force the clean water tile upwards to reduce the pressure. Removing the layer of clean water makes the polluted water act as I would expect.
Part of the 1 element per 1 tile factor of the game I suspect, as if there is more than 1 tile of clean water above the polluted water it again expands to rest as a more reasonable pressure.
However I'd not seen it occur with the bottle emptier and it came as quite a surprise to find my cistern break with what looked like a tiny volume of liquid.
Steps to Reproduce
Polluted water tiles, with a clean water tile on top. Then increase the mass of the polluted water tiles via either debug or bottle emptier.
This issue has not been confirmed by a developer yet.