Well basically I created the missile pod shape, but half of it went though the main body - so it would not be visible. I then used whatever tool* it was to remove the parts which were inside the main body, therefore they should be no polygons passing though one another.
*The symbol is two spheres, one green and one red, joined. One is lighter in colour than the other.
When you say 'effect is caused by polygon intersection' do you mean than the polygon forming the slope of the pod is passing though the polygon making the side of the helicoper body? Shouldn't intersecting a cube around the whole model remove excess polygons and prevent this?