Recipe book possibly loses items if items are picked up during crafting. Here's how to reproduce this. First, run these commands on a player with an empty inventory, in this order:

/setblock ~ ~-1 ~ minecrat:crafting_table
/gamemode survival
/give @p minecraft:diamond_hoe 28
/give @p minecraft:iron_ingot 576

Now you should have a full inventory and a stack of iron on the floor. Then, open up the recipe book and shift-click iron block twice. You should now have lost a stack of iron from your world.