Hi Ray,
As I have noticed the "dead zone" is used to hide a form element when you "delete" it using Designer.
And I believe there are some important reasons do not remove them from the form at all. First, the system still have hidden field values for query processing on form submission. Next, removed element custom settings will remain if you would like to display it again. So I strongly suggest do not remove elements from this zone manually.
From the other hand the Designer tool is still not perfect and have some issues I think. This could happen that controls are doubled in a form when you try to add/move/remove them. So if you have found some duplicated reference you should remove it manually. Please be very careful to avoid html integrity damage when doing this.
Gytis