If I remember correctly, they used up too much fuel from their thrusters just getting close enough to him (since he had too much drag to get high enough into orbit for them to snag him), but then realized that they were coming in too fast to snatch him. So in order to slow the ship down, they depressurized part of the ship via a makeshift bomb, forcing out loads of air on a contrary vector, slowing them down just enough to send in their space walker and reel in Watney.