I believe these black areas are parts of the mesh that are not visible in any photo due to:
1. being masked out
2. being occluded by the mesh from every camera angle
3. outside the field of view of any camera
If you export the orthophoto as TIF or PNG, rather than JPG, then the black areas will be transparent.
In this case i think it is most likely issue #2 above, and you probably have a noisy mesh in this area. You might do better by either smoothing the mesh (Tools->Mesh->Smooth Mesh - but save first as you can not undo this operation) so there are fewer lumps and bumps occluding certain areas, or just build the mesh from the sparse cloud so it is lovely and smooth to start with.
Have you tried the ground point classification tools? They might also help avoid a lumpy mesh caused by meshing things like trees etc that protrude above the ground and cause occlusion.