It’s likely appearing when you make the mesh, and if you aren’t seeing it in another application it is because the application has “smoothed them” so they don’t show.
Mesh toolkit and convert the mesh to solid. Based on the model I am fairly certain it will fail to build a solid as your geometry is disconnected.
Instead of a mesh or fighting importing the world, why not build a single surface for the upper ‘top’ and a second surface for the base of each mass portion in Rhino in two new layers. Then bring those into Dynamo by only importing the faces on the layerS with Rhynamo. Get the distance from the top surface to the polysurface below it. Then extrude the top surfaces by that distance in the negative Z axis. Union the geometry into one solid and then import that.
All of this will be slow as you are working with three or four geometry engines here, as well as 3 conversions. Be patient with it and run it in sections, using a remember node as required to serialize the good data into the DYN to simplify things as you go.