Hi Eric,
there is a difference between inner Faces and intersecting Geometry.
Here the left Cube has an Inner Face (often a big problem, should be avoided), while the two Cubes on the right are just intersecting and the selected Face is not considered an Inner Face (intersections like that are not pretty, but if not visible in close-up, more of a “who cares”. You can still Delete that Face and leave the intersection.):

Basically, the problem is, when an Edge is connected to more than 2 Faces:

I hope that helps.