Comentario oficial
A negative calculated volume will show when you draw the polygon around the rim of a pit as you have with your big annotation. Picture a sheet of plastic being stretched between every point you select for the polygon. We count all of the ground that within that area that is above that sheet as positive and the air below it as negative.
This is the same issue you are experiencing with your smaller measurement area. Since all the ground is not on a level plane, some is below the calculated surface and some is above. This will give you some weird results.
The volume measurement tool is designed to work with a pile of dirt on a level surface. It is possible to measure negatives.
If you draw the polygon on the side of a sloped surface, the reference surface will follow the shape of the hill and likely come out somewhere near zero.
