Sagan has been the fastest racer at the end of two stages, fastest by good measure. Just like Kittel has been winning his stages, Sagan should have won at least one of the two stages he was fastest in, he is a pro and its his job to finish. He is more sprinter than opportunist, so judging the Nibali situation was hard on stage 2, but I think the stage 2 race was on his mind and he tried too hard early and then tried to rest too much assuming he didn't have enough left to sprint early. Sprinting on a stage like today requires a longer sprint because it is the tour and a hard stage with no other sprinters left, he burned an early match and either didn't have it or waited too long assuming the sprint would come to him. I personally just think he waited too long to start, his position at 300 meters was perfect.
While I agree it is bike racing and anyone can win on any day, when it comes to more select groups and you are the only sprinter left, you should be winning the stage.