Since the surfaces and subsurfaces in EnergyPlus are defined by using the four corner vertices, it is very easy for the subsurface (doors and windows) to not be on the same plane as the surface (wall, roof or floor) that they are supposed to be part of. The outward facing angle is the imaginary vector that points outward from the surface or subsurface. If the subsurface and surface are on the same plane, the outward facing angles would be equal. The warning message is saying that these angles are not the same.

The second portion of the warning message is saying that you can put the Output:Diagnostics object in the file with the first field being Display Extra Warnings. This will give you a little more detail in the warning message and name the surface and subsurface that are causing the problem along with the title and azimuth angles for each surface. This will help diagnose the problem.

As Amir suggested, you might want to use a tool to visualize your IDF file such as the Legacy OpenStudio plug-in to SketchUp.

The newer OpenStudio SketchUp plugin has a Render by Surface Normal render mode (no toolbar, but it is in the menu under "Extensions/OpenStudio/Rendering"). If you are using the legacy plugin you can do this by going to SketchUp's "Style" menu as shown below and rendering by then altering the front and back face color. (Pick second cube to access "Face Settings" and then for style pick anything but first two cubes)

To fix any problem faces you can right click on one or more faces in your current surface group and choose "reverse faces". It would be nice diagnostic measure to automatically find and fix these, but I don't think one exists yet.