Clay pits keep flooding and disappear

[Ida]

I have the city settings set to "not flooding" for clay pits, but nonetheless my clay pits keep getting flooded. Also, when they do, they go invisible. They're still there; I can't build on the spot where it used to be and I have to clear it first, but it looks like the tile is vacant.

[Joshua Ginsberg]

Also happens with the Gov's house.