I thought he just got left in a bad place by his leadout. It looks like the wind was right-to-left, so first he had to bump shoulders with Stewart to hold Boudat's wheel, then Boudat's positioning ended up giving Viviani an extra bit of time in the draft after his own leadout had pulled off, while Bouhanni had to come the long way around Boudat to follow Viviani.
I mean, he probably shouldn't have nudged Stewart either time, but once he saw Viviani go it was last-chance time. After that he just seemed to sit on Aberasturi's wheel to the line, I think he knew he was getting the heave-ho after the finish anyway.
I think if Arkea could do that sprint again, they'd try to come up on Cofidis' other side, or have Boudat pull off to the right, block Aberasturi, and give Bouhanni a clearer run while giving Viviani less shelter.
And that matches with Bouhanni's
apology; (my italics)
And I think that's the difference between good leadout men, and great leadout men. It was a real show of strength for Boudat to bring Bouhanni up the windward side and take him to the front, but he left him with no clear run to the line. You don't see Morkov leaving Bennett to go the long way around, or Richeze blocking Gaviria's path. Mark Renshaw would've gone hard left to cut Viviani off and make sure nobody got in Cav's way.