intersecting meshes results to mesh with wholes

I am using THREE and I am trying to intersect a box mesh with a custom geometry I am creating and converting it to geometry using :

const g = new THREE.Geometry().fromBufferGeometry(shape3d)

I aim to add faces to the custom geometry, that is why I do that. So I expect to get back from the intersection my custom geometry + polygons that the box has.

I get that indeed, though I get also some holes as you can see in the below image :

I used many csg versions that are out there, the manthrax one, the ThreeCSG etc but no luck!

thank you

I suggest you set bevelEnabled:false to your mesh extrusion, because I am psychic and I can see your code in my head. :D