How to reproduce:

1. Place a chiseled bookshelf
2. add a book to the first slot (top left)
3. standing on top of the block, execute 

   /item replace block ~ ~-1 ~ container.0 with air

-> the book will not be removed

Removing an item like this works for every single other block entity container in the game (except for jukeboxes, also being affected by this since being made a container block entity).

Possible fix: Update the if clause in the setItem method in ChiseledBookShelfBlockEntity to allow empty items