EnergyPlus simply does not like zones which are 100% within another zone. This is typically due to a courtyard, but could also happen with a conditioned space. Below are a couple examples of a zone within a zone. The top image is a SketchUp model which has a true courtyard and the bottom image is of a Revit model which has a conditioned zone within another conditioned zone. Looking at the Sefaira zoning tab output on the right side of both images, an additional "wall" has been added which is circled in red. Below the images, we will explain what this wall is, and why it is needed for EnergyPlus to work. 

The wall which needs to be added has no affect on the the analysis and is constructed as a Zone Separator Construction wall type, which means it is an adiabatic surface. 

(Image from OpenStudio after downloading the .idf file from Sefaira)

Why do we have to do this? 

As stated at the start of the article, EnergyPlus has limitations which drive the need for the additional wall. Using the SketchUp courtyard model as an example, without the added adiabatic wall there are roughly 15 vertices making the outer loop of the floor plate, and 4 for the inner loop. This is exactly where EnergyPlus has an issue. It does not know how to treat those two loops as one, and with out the added adiabatic wall, would end up creating a zone for the courtyard section which would add unwanted square footage to the project. 

With the additional wall in place, the floor plate can then be created by an uninterrupted string of vertices.