It isn't that the points are inverted or actually negative. It is hard to triangulate locations from multiple images when things are moving. Sometimes the solution comes out to be in an unexpected location (ie below the ground) if something isn't in the same place in two different images.
Using images to reconstruct a 3D scene has to Achilles heels: trees and water. Water is almost never still and if it is, it has a lot of glare issues. Trees are going to be moving in any amount of wind.
If more overlap doesn't do it, flying higher will fix the issue with trees and can help a bit with water. Or only map treed areas on the stillest of days.