"Put into graveyard" versus "exile graveyard"
Kind of.

When Emrakul hits the graveyard, his ability 


  When Emrakul is put into a graveyard from anywhere, its owner shuffles
  his or her graveyard into his or her library.


goes onto the stack. Then priority will first go to the active player and then to the other. After receiving priority, Tormod's Crypt can be activated.


  Exile all cards from target player's graveyard.


All cards go into the exile zone.

After that, Emrakul's trigger resolves, and its controller will shuffle his or her empty graveyard into his or her library.