While retopologizing a human head, the internal cavities i.e. nose, mouth, ear, eye lids, were extruded inwards to create the required occlusion effect. While all the mesh is in quads, the final face in these cavities is an N-gon. After applying the multi res modifier at latter subdivisions, the single ngons turn into a jutting irregular triangular mess. Even when smoothed in to disappear in sculpt mode, they retake their shape at saving or changing modes. Is there anyway to exclude these n-gons or subvert this effect without doing major changes to the retopology? Can I at least prevent them from penetrating to the exterior?
What I would suggest is turning the faces into quads or tris, like by poking (Ctrl+P). I don't know how exactly you want to save your original topology, but this shouldn't visibly change anything from the intended shape.
Alternatively, if you're sure nobody will ever look up the nostrils (if this is a demo render, etc) then you could just remove the faces. however, if you're planning on texturing it open holes in the geometry can cause problems for volumetric or subsurface shaders.
Is there any overlapping, inverted, or otherwise crunchy geometry? I would check for inverted normals but other than that I think this is almost definitely a bug. From what I saw it looks like your geometry is neat enough that the smoothing subsurf algorithm shouldn't be confused by anything on your model.