Hello Ben,
Holes usually appear in the areas where there's insufficient information related to the surface (usually areas of no overlap), so PhotoScan has no depth information for such areas and cannot generate the surface that will be following the terrain.
However, you can use Extrapolated option in the Build Mesh dialog to generate the surface without any holes - in this case the polygons that are filling the gaps will be considerable smaller than ones used for the Close Holes operation, and would look more naturally.