It's due to a bug in XCode Interface Builder. And in my experiments it's been predictable according to the following explanation:
The lighter colored area is intended to highlight the container view of the current selection. So it you have an NSTextField within an NSBox, and you select the text field, the box will be highlighted. It's purpose is to dim out everything outside the scope that you can currently make constraints in.
You can see that it's a dimming down of everything outside the box, as if nothing is selected, the whole IB view port is displayed in the lighter shade.
The bug is that when you make a selection, IB clips the area of the container view to what's currently visible, and then adds this highlight as a rounded box 8 pixels larger. But when you scroll or resize the IB viewport, this clipped area isn't updated. So the rounded highlight box is seen to not cover the whole of the container view, just a clipped part (plus 8 pixels) of it.