The fact that countless hunters (including Jacob's and Maisie's parents) and sea beasts died in a pointless War for Fun and Profit that lasted for centuries and only served the greed of the monarchs. The bottom of the ocean is full of sunken ships and the bones of dead sea beasts, and each and every one died for nothing.
The falling-out between Jacob and his Parental Substitute Captain Crow is hard to watch. While Crow eventually realizes that Jacob was right, in the end, they never get the chance to reconcile.
While the end of the Age of Hunting is a good thing, many hunters like Sarah Sharpe face a very uncertain future now...