I think the referee did a good job deducting points from Nathan; he just didn't react to the last infraction, the piledriver. I think it was because there were only a few seconds left in the fight. I feel that Nathan should have been disqualified; this is not the first time he has committed such an infraction. I remember back when he fought Cachorrao (Ricardo Almeida) for the Pancrase title; Cachorrao choked out Marquardt and he punched him several times after the stoppage. Renzo (Gracie) jumped through the rope and kicked him two or three times for the cowardly move.
Here's the infamous Renzo Gracie-Nate Marquardt altercation he's referring to: