So why are some windows on this building automatically getting filled with the black color?

excess layering could be a cause but i can't tell without inspecting the fla and even that may not reveal the cause.

it's probably quicker to just recreate the problematic parts but how you should do that also can't be determined without the fla.  in general, if all the square windows are supposed to be the same shape, create a movieclip or graphic symbol and reuse it for all 8 of the square windows.