Well, he was trying bloody hard to pass all those bikes, degradation must have played it part. Plus that closing a gap of 12 seconds in 18 laps would be a miracle, so there was not point in trying like crazy.Rossi's gap to the top3 got bigger after he was past Dovizioso, not even sure if he had been able to beat them without penalty. Imo he lost it in Misano when he waited too long to switch bikes.
That wasn't standings, but those which led to the start from the back (a bit similar to the F1 penalty points system). Iirc he had already one, else nothing would've happened I think.(3 points for pushing another rider off line?)