I was working on a new design and did not want to take a long time to generate the initial map so I chose to set low noise, no cliffs or erosion. After I had the map completed to the initial layout I then added some noise, cliffs and erosion to the design map. When the map generated no cliffs were shown being generated below sea level. To verify this I made a new map and selected to generate it again and the same thing happened with the cliffs. To test this as a possible problem I generated a map with normal settings and then changed the design map to no cliffs. The map generated cliffs below sea level but not above as was selected.
My version is 2.9 pro beta so maybe it is fixed.