Usually, the only reason for the extra lines are modeling and layer combination errors. Never be sure that something aligns - check it. Automated systems are merciless - if you don't do EXACTLY what should be done, you will not get what you want.
I also have a feeling that the CP definition can have a lot to do with your problem. Post a part of the 3D view, and the elevation - then we could be able to decipher something.
Djordje
ArchiCAD since 4.55 ... 1995
HP Omen