I go to a college with a top-5 polisci grad program, and I've talked to some of the profs about why/how this happens. They basically said that every year they make a first cut from the 4-500 applicants down to 60. That part is easy. Bad GRE's, fluffy classes, bad statements of purpose. From the last 60 on all of the students are of almost indistinguishable quality. They're all so good on paper, it's impossible to tell which ones will be good in grad school.
So from 60 down to the 20 or so who get in, it's almost all luck. So suppose there were 60 "good" applicants in the entire country, and they each all applied to the 10 best places. If the process is completely random, there will be a few people in the right tail who get in everywhere, and a few in the left who get in nowhere, and people in the middle who get into some random proportion of the schools.
Of course the process isn't entirely random (I'm sure there really are some applicants who get in everywhere because they are head and shoulders above everyone else, but I doubt there are many people like that). But that is the main explanation for why things seem somewhat random...it's because they are! So people who get in everywhere shouldn't get too high on themselves, and people who get in nowhere shouldn't get too low on themselves.