Do you mean two zones next to eachother with a slight overlap, or two identical zones sitting on top of eachother? For the last one you can install the Check Duplicates tool from Help > ArchiCAD downloads.
For the first one if you make sure that there are zone boundaries setup (walls, collumns, curtainwalls, polylines, etc) you can use the Inner Edge method of automatic zones and should never have overlaps.
We use the following system (a visual check - sorry, doesn't seem to be a way to automatically audit using ArchiCAD)
1. Set each Zone to have cover fill ON (50% foreground pen and zero background pen), and Zone contour line ON (we use a 0.25mm red pen)
2. Set a model view option (pre v20)/graphic override with no zone category fill
Overlapping % fills show up as darker colour. If the zone boundaries are not correctly aligned, the contour lines also make this obvious
The easiest solution that I also pointed out 5 years ago is to use zone boundaries with automatic updating, rather than manual drafting of zones. A lot of elements can operate as a zone boundary. Ussually these are walls and collumns, but a line or polyline can also be set as a zone boundary.