It's a sorting/rendering issue. Transparent polygons have to be z-sorted to be rendered in the correct order. That ordering is done by the so called painter's algorithm, which doesn't ensure a perfect ordering. There's not much you can do about this. Splitting the object, i.e. separating the bottom from the rest and playing around with Object3D.setSortOffset(); may be an option if the object usually isn't visible from all sides.