It looks like all you need to do is change the pitch of that smaller bit of roof so it joins correctly.
In the 3d window, click on the very top node, then select the 'Adjust Roof Slant Angle' button in the pet palette, then just snap to the corner node of the main roof. You may need to temporarily adjust the smaller roof so it is lower as it could cover the node you are trying to snap to.
The reason they don't join up in 3d is because the hip line isn't at 45degrees on plan.