In my experience of scanning small figurines (
https://sketchfab.com/nikska/collections/sailor-figurines), the top and bottom chunks may not correctly merge or be aligned do to the optics used and possible focus breathing.
I found it ideal to try and keep the constant distance from the object center for both chunks and avoid smaller focus distances for macro lens.
Another issue is the lighting mismatch for both chunks, but this results mostly in an uneven texture rather than incorrect model.
So, as a rule of thumb, after an incorrect merge, I was making a full new run with the fixed focus trying to reposition camera rather than changing the focus. Also make sure you are using prime lens, this eliminates even the slightest probability of changing optics geometry.