When 2 aquifers intersect, the layer of stone separating them should go down to the bottom of both bodies of water and separate the 2 aquifers completely. (shown in screenshots 6-10)

However, as of snapshot 21w08b, the layer of stone separating the 2 aquifers stops just above the water level of the lower aquifer, resulting in a floating line of stone between the aquifers. (shown in screenshots 1-5)

 This is the case for all aquifers which generate intersecting each other.