@nateshanes01 Roofs can be really tricky. So choosing the right one for a given situation and the order in which you do things plays a part to keep things like what you have from happening.
In this case, I suggest you change the roof that appears in the picture to a half hip roof rather than a full hip roof. That way you can keep it from intruding into the area with the fence.
The other thing you can do is get the inside walls and fences done before applying a roof. And you may have to add the roof in sections too.
Also, when you draw a fence rather than use the option to replace or change a wall to fencing, that helps for certain things too.
Hope this helps.