This isn't a bug, just regular behavior of OpenStudio/EnergyPlus. In EnergyPlus, the concept of OpenStudio Spaces doesn't exist. Only thermal zones matter.

So historically in OpenStudio if you model separate spaces and include them in a single thermal zone, the area from the upper space is excluded of the building Floor Area. According to this answer, "OpenStudio does this for any interzone floor/ceiling surfaces whether they have an air wall construction or not".

I just tested in OpenStudio 1.9.0 (Release candidate), and it is still seems this may not be the same behavior. case anymore. I applied a single zone to two spaces right above each other in the Sketchup plugin, and then I used it counted the "Surface Matching Tool", and OpenStudio did exclude the top space.area of both by default.

Note that using the Surface Matching tool is very important to have this behavior, if not matched, the area of the top space will still be included (but your heat transfer will be wrong).Here are my thermal zones:

You could set the ceiling of the space below and the floor of the space above to Adiabatic (and assign construction) and it will count the area of both, I just checked.

This isn't a bug, just regular behavior of OpenStudio/EnergyPlus. In EnergyPlus, the concept of OpenStudio Spaces doesn't exist. Only thermal zones matter.

So historically in OpenStudio if you model separate spaces and include them in a single thermal zone, the area from the upper space is excluded of the building Floor Area. According to this answer, "OpenStudio does this for any interzone floor/ceiling surfaces whether they have an air wall construction or not".

I just tested in OpenStudio 1.9.0 (Release candidate), and it seems this may not be the case anymore. I applied a single zone to two spaces right above each other in the Sketchup plugin, and it counted the area of both by default.

Here are my thermal zones:

Here is the top space selected, with the option to set it as 'Part of Total Floor Area' highlighted: