To make it clearer, I don't have a FB account but from what I get from the article:
John add Bob in his friends.
Alice add Bob in her friends, and while crawling her contacts infos (say, on her smartphone), facebook finds a phone number for Bob that Bob himself didn't give.
Facebook remember the phone number on Bob's "shadow" account.
John download his infos, and for his friend Bob he can see the phone number. Bob never gave it to Facebook, never gave it to John. Facebook never told Bob they had it.
John add Bob in his friends.
Alice add Bob in her friends, and while crawling her contacts infos (say, on her smartphone), facebook finds a phone number for Bob that Bob himself didn't give.
Facebook remember the phone number on Bob's "shadow" account.
John download his infos, and for his friend Bob he can see the phone number. Bob never gave it to Facebook, never gave it to John. Facebook never told Bob they had it.