Intersecting 2 orthogonal faces should be simple and foolproof, right? - so how does an Intersect Faces with Selection result in the corruption of both faces by the creation of many spurious lines of triangulation - insidiously hidden by SketchUp unless you happen to have View Hidden Geometry active!..
An admirable sentiment, but…
I assume you mean planar (or that the vertices are not co-planar), and you mean both faces since they were both corrupted…
Both faces were created using SketchUp functions, and were accepted and stored by SketchUp as planar faces. In fact, if you delete all of the invisible lines, SketchUp will typically still present both faces as planar.
You are indicating that the one face has vertices out of plane by 10,000ths of a millimetre!..
In the real world, I’m not sure that anything can even be manufactured to such a tolerance (so it seems sufficient to me), but, if you could perhaps explain how I instruct SketchUp to model even more accurately and consistently, I will of course be able to do likewise.
Until then, this is a SketchUp defect, requiring the attention of the SketchUp developers.