You can either:

• Select the Dissolve unwanted edges and/or Dissolve unwanted vertices. This built in optimisation may help.
• Alternatively, before adding the windows, add an extra extrusion or edge loop to the top and the bottoms of the cube.

These artefacts occur due to how the window generator splits up the mesh when determining the windows to add. 

If you are still having problems after the following suggestions do not hesitate to contact me and we'll discuss. There are two main possibilities:

• It is likely that the face is an irregular shape (in other words, not very rectangular).  This is because the tool works best when creating windows on more rectangular looking faces. By default, the windows are applied to each face from the top edge to the bottom.  See the documentation tab for further details.
• By default, the window generator will dissolve unwanted edges when a window pattern is created.  Often, this can reduce the complexity of the mesh but sometimes it can create undesired effects.  Try disabling the Dissolve unwanted edges option, and if it is selected, turn off Dissolve unwanted vertices as well.

I would suggest towards the end of the modelling stage, where all the details have mostly been modelled and the overall shape has been defined.

This is most likely because although the adjacent face looks like a quad face (4 edges, 4 vertices) it no longer is.  This is because the windows added to the face you selected previously has added extra vertices.  Instead, try selecting both those faces and create the windows in one go.

The add-on works on quads; that is, faces with 4 edges connected by 4 vertices.

The higher the subdivisions the tool has to make on each face, the greater number of calculations the CPU has to do.  This can become worse when Bevels are added to each window, as Blender has to do even further calculations per window.  You can decrease the chance of this locking out Blender by disabling Bevels completely (by setting the Bevel amount to zero).  I thought about putting a restriction on how many windows you can create, but I felt this limited the tool.

I would welcome you contacting me through this website, visit www.markkingsnorth.com, or through twitter @markkingsnorth.

Make sure you are in Face Edit Mode. As the Operator works on faces, the option is only available in that mode.