The problem is with the game mechanic itself.
Only the highest roof on top is counted as "roof", all roof parts that get covered by that higher roof will dissapear, eg. the top roof you created there overlaps with the corners on the roof beneath it, so the corners dissapear as for the game "there is a roof on top of it".
I havent found a solution anywhere for that as I had the same issues with more complicated buildings. Maybe someone knows D: