I develop C# plug ins using RhinoCommon. I have noticed that the Rhino6 Mesh Split and Mesh Intersect functions no longer work the way they used to in Rhino5.
(i.e. when running a mesh split in Rhino 5 it will successfully split the mesh, while in Rhino 6 it actually deletes one of the split mesh pieces)
As you could guess this is a pretty big issue.
Similarly with the Mesh intersect command is malfunctioning. The Rhino 5 would return one polyline that follows the contour of the mesh, The Rhino 6 version starts the polyline half way through the mesh and continues along the contour, and jumps back to the other side of the mesh to finish the polyline.
I would guess that these two issues are somewhat related. Considering they both use the same type of algorithm under the hood.