In 3D document, right click and open 3D Source and change the 3D window to internal engine and see if you see these extra bits.
In 3D document, turn on colours (uncut own surface colours) to try and determine what those bits are.
Are they selectable in the 3D document and what element do they belong to if you can select them?
Hope that helps.
James Badcock
Graphisoft Senior Product Manager