The easiest way to reproduce it is by resizing. For example, if you have an existing area and are resizing it, the process is to right click on the area target and drag. If a dummy like me right clicks and drags up and to the left to the point where the area disappears and let's go of the mouse, an area is generated that persists through multiple page creations, but is unusable and undeleteable from AC, yet still generates the yellow border. There may be other ways to create the effect, like dragging an area off the picture, but I haven't tested that.
I'm not sure if it's realistic to prevent this from happening. Nothing is foolproof, because there are always better fools. One method may be to have a minimum area size.
Just being able to resolve the issue through AC would be fine rather than trying to prevent it though, like a "clear all area entries" option.
Wolf