Murray was serving at 3-3, 30-40, and footage confirmed he served a double fault. That should have given Nadal the game, but instead Murray saved the break point and won the game. Nadal would have been serving up a break, so I think that it made a big difference in the outcome of the set, maybe the entire match. Nadal could, and should have challenged, but ultimately, the umpire and lines people are responsible, because this is their job.
Not really, this is why we have the challenge system. Nadal should've challenged, and has noone to blame but himself.
Besides, its pointless speculating whether or not Nadal would've won had that happened. Murray was the better player on the day, and would probably have won anyway.