When a mesh has a vertex with 3 or 5 (not 4) lines connected to it, after some sculpting the vertex often shows up as slightly higher or lower than the surrounding vertices, regardless of how careful I try to smooth it, it still stands out awkwardly. The Flatten brush seems to be able to get rid of the irregularity. But why can’t Smooth work?
ZBrush’s features are optimized for standard polygon structure of four quads sharing a point. Non-standard intersections will create this effect. I don’t know what the exact reason for it is, but you’re already using the Flatten brush workflow that eliminates those dimples after they form.