Mostly the swift exposition at the end with the letter. It's a cheap literary device and it's just so jarring in contrast to how well-handled the rest of the film is. Plus, a lot of the closing dialogue is straight up terrible. The bone guy added a really awesome layer to it, but a lot of the ending feels poorly slapped together to tie up loose ends. I think that Flanagan could have written another act that told the same story in a less corny way.

Also from what I hear, the traumatic event is a lot more graphic and violent in the novel.