Hmm, that's interesting, I didn't realize that Us Weekly had hired the photographers. Still, in this case, isn't Us Weekly essentially functioning as the stand-in mother agency? Perhaps Stewart's team couldn't have negotiated with paparazzi agency itself, but surely they could negotiate with Us Weekly to withhold certain photos. It seems that the evidence in fact points to at least some degree of this taking place. There was talk of a batch of 50 photographs being published, yet as far as I know, that never took place, and though that batch was accidentally leaked online (goodness knows how), they were immediately and mysteriously pulled from all sites on which they were published.
Even putting those facts aside, there are two considerations suspiciously incongruent to the notion that Stewart's team wasn't able to withhold certain photos. Being the highest paid actress in the world, Stewart would have offered up obscene sums of money to ensure that certain photos were never made public - surely whoever was in control (whether it be a magazine, paparazzi agency, or anything of the sort) would have taken the bait and tried to cut as large a deal as possible. More plainly though, consider being in the position of the paparazzi on the scene. Fifty photographs is hardly more than what results when a celebrity of Kristen Stewart's caliber poses on the red carpet for sixty seconds. One paparazzo, much less three, knowing that capturing the perfect shot will lead to the single largest payday of his/her life, would not simply stop at fifty and consider himself safe. In that situation, I should think that fifty would be the wrong order of magnitude.
I'm not familiar with the modus operandi though, so please feel free to correct me if that's unsubstantiated.