First of all, this render of yours is VERY cool! Can I share it on my Twitter (with credits of course)?
About those issues - that's how the viewer works. I don't have many tools for procedural mesh generation (in Away3D), so, for example, a gatehouse is just three boxes combined without trying to clip anything. I probably can (and should) fixes gatehouses, but walls are harder. If you take a look at exported mansions you'll know it can be much worse :)