Here's something I find useful when something unexpected turns up in a section or elevation drawing:
If you select the section box in the 3D view and switch to a plan view, the extents of the section box will be visible in the plan view. You can then adjust them to the approximate line of the questionable section or elevation. Back in 3D view, you can then rotate the model around to get a better idea of what's going on.
Here's an example:
1. Weird rectangle shows up in elevation
01.png
2. Hovering mouse over it reveals that it is a skylight. It doesn't look right.
02.png
3. Determine location of elevation
03.png
4. Go to 3D view. Activate and select section box.
04.png
5. Go back to plan. Section box and control handles are visible.
05.png
to be continued....