How do I prevent this?

I would just pull the roof into the house further, as counterintuitive as that might sound. It can sometimes cause bugs, but usually the part of the roof inside the house just disappears.

LucyLovesMarvel​ That's a pretty common issue when you build in an attic space.  Sometimes redrawing the wall will fix it but a lot of times it won't.  So, the way to fix it is to break the roof up into sections and use half walls along the edges with a higher roof above the top of the rooms where you can.  

Hope this helps.