There may be other (invisible) obstacles, or wrong collision polygons, or the cells size is too big.
Impossible to tell without seeing your capx.
other (invisible) obstacles - no
wrong collision polygons - what you mean? polygons of obstacles? They don't interfere with the polygons in the bottom obstacles, so I think it'ok.
cells size is too big - no because the bottom obstacles do not bother them. They like bottom are like in gravity