Topologically correct polygons in the same layer should never overlap. Overlapping polygons in the same layer can result in some (typically smaller) polygons being completely hidden by an overlapping polygon at certain zoom (scale) levels. In such cases, polygons can appear, disappear, and reappear at various scales. This is because with SQL database layers and file layers using R-Tree spatial indexing, the order shapes are rendered (the overlap order) can vary at different scales.
Topological rules require logical organization of polygons shapes by feature into different layers, so that any overlapping situations are represented by polygon shapes held in different layers. For example, property parcel polygons should be held in a different layer than polygons representing building structures situated on the parcels.
Consider using the TatukGIS Editor Topology Builder feature to systematically clean up topological errors in polygon and line layers. Polygon topology errors typically involve overlapping polygons or accidental empty spaces between adjacent polygons sharing the same boarder. Line topology errors typically involve not closing intersections, missing intersection nodes, and dangling line endings. Refer to the Editor Tools / Topology menu helpfile topic for more about this feature.
Polygon winding is also important. Topologically correct polygons must have clockwise winding. Any topologically correct hole within a polygon shape must be formed by counter-clockwise winding and as a part of the polygon. (So a hole within a polygon cannot be formed by a separate, overlapping, polygon shape.) See related knowledge base item KB10469.