Hi Andrew, thank you for looking into the issue of strange geometry when using symmetry with Autopo. I've done a bunch more testing of Autopo and I've noticed a few things.
If you start a new voxel sculpt, choose the large sphere, then use Autopo with a 400 poly count (without turning on symmetry) - there will be duplicate vertices over the mesh that line up with the vertices along all three axes.
If I create a sphere and use symmetry, then the duplicate vertices are only along the axis of symmetry. If I create a sphere and use symmetry along two axes (x,z) then there will be duplicates along both axes.
I also discovered that if you use the Select tool in the Retopo room, pick vertices then click the delete this layer in the Poly Groups window it will crash 3D Coat. This doesn't happen if you select edges or faces.