Why does my mesh have random objects below ground level?

All of my meshes I create in Context Capture have all sorts of random objects below the surface/ground level. Everything looks good from on top but it looks a mess underneath. The same goes for the underside of tree canopies that have no data. In my latest model I have a large residential section with some buildings and a lot of vegetation. I have a lot of random objects below ground such as pieces of building roof (corrugated iron) and also the underside of tree canopies is corrugated iron.

Why this mess? How do I stop it happening?

Thanks

Caleb