When you sketch a Roof by Footprint there are some very specific differences and behaviours between using the 'Pick Walls' option vs the 'Lines' option. Once you are educated on how they both work you will be much less confused on how your roof(s) are behaving as well as how to fix the problems without design comprimise.
Below is a direct link to a short Video Tutorial on this very topic. Even an experienced REVIT user may learn by this lesson.
You can right click the link above and click "Save Tartget As..." to download the file to your desktop or share with others.