Carlos, if you are using the legacy OpenStudio plugin and are within a zone, and copy the zone geometry up on top of each other you would see odd behavior. Generally zone geometry should be an empty shell with no extra surfaces included. In what you describe you would end up with two or higher story shell as a single zone, with multiplier surfaces floating in the middle. SketchUp can't have two surfaces in the same position with the same grouping. As a result you are probably ending up worth the middle surface being defined as a roof, and not a floor, and that area is not counting towards the floor area. It is also possible that the floor at the bottom is defined as the wrong type of surface which would affect the area. If you want to make a multi-story building in the legacy plugin you want to be outside of the zone group when you copy it so you are copying no just the surfaces but the group container as well which will make additional thermal zones.

The same logic of copying and pasting within a space applies to the current version of OpenStudio. While multiple spaces can be put into a zone, each space should be an empty shell. In this case if you want to have interior surfaces you can model them as interior partition surfaces, which look much like shading surfaces, but which can become internal mass objects in EnergyPlus. This is in fact what happens to common surfaces between two spaces which end up being part of the same thermal zone.

This question does touch on one condition that some users have had in the new OpenStudio when combining multiple spaces into a thermal zone. The most typical use case is having multiple adjacent spaces on the same floor combined as a zone. In that case the floor area of the zone matches the sum of the spaces. The shared inter-space walls become internal mass objects. We have had some people stack spaces vertically that are on different stories and combine them to a zone. In this case shared surfaces between the spaces are also turned into internal mass objects, but in this case we have an issue that the floor area of the zone isn't the sum of the floor area of the spaces. One solution we have talked about to support this is overwriting the "area" field in EnergyPlus with an OpenStudio calculated area. We could look at the floor construction used to see if the intermediate floor surfaces were intended to be real, or were stacked to mimic an atrium. We would do this by looking for an "air wall" construction, and not adding area if the intermediate floor uses that construction. If someone had to do this today, we could write an EnergyPlus measure to overwrite the area. Of course the user could also just model a single thermal zone and set the zone multiplier within OpenStudio.