We don't know how many sentry robots may have been destroyed during the mutiny, it could have been a close run thing. Old BOB was the last survivor of his kind on the Cygnus,
itseems to me he and his type would have also been on the side of the crew. Unless of course, Reinhart suspected the jig was up, and did some reprogramming of them to support him, from BOB's and VINCENTS combat prowess, having them on his side would have been a considerable asset.
The existence of the humanoids make me suspect that maybe Reinhart used some kind of disabling gas? A flashback to the mutiny would have been nice, but really would not have served the plot much.