I havent' read the article, but I am wondering: If iPad is trademarked (is it?), then why do you need to trademark "iPad whatever"?
The application did not disclaim a trademark in "Mini" used alone. That is one reason why it was denied. If it had been allowed, Apple would have been able to claim infringement for every product that used the word "Mini" in its name.
Apple will need to correct its "error" when it resubmits the application.