This sounds really fishy, since the Common App is not set up to allow two ED applications to be generated from within their system. The student or the counselor would have had to do a withdraw/bypass for the second ED application to even be submitted, or performed some sort of application over-ride, which makes this deliberate flouting of the rules more concerning…
Perhaps this was a circumstance of both Common App. ED, and a Coalition app. ED?
I know U Penn only accepts Common App, while Northwestern accepts both.