Graduate admissions are very different than undergraduate admissions. In undergraduate admissions, you can generally predict where you'll be accepted and where you won't. But graduate admissions - particularly PhD programs - are significantly more complicated. Because of quotas and financial obligations, they have to try to pick, on the first round, students that they actually think will attend. The reason for this is because, once they make a financial offer, they know you can hold on to it until April 15 or something, and during that time, they can't allocate that money for anyone else.
So, if they see someone who is easily qualified for the school, but they suspect will get other, better offers, they'll likely just pass on that person in the first place, since they don't want to commit money to someone who won't end up attending. If they are mistaken about this, they may end up with a small and/or weak incoming cohort.