I assume you used the polygon method to do each plane seperately?
Using the Polyroof method (see user guide), i think, would automatically sort out most of those hips automatically (assuming all pitched equal). Would still need to adjust for extended eaves at bottom right.
To adjust hips as shown, select one of the roof planes you want to adjust, then select roof tool; holding the CTRL key (for PC, equivalent for mac) click on the edge of another roof plane you want to trim to the selected roof. Repeat as required.
