General scenario: A player has a full inventory with additional items at their feet (which cannot be picked-up). If the player tries crafting a recipe using the same ingredients as the dropped items (by Shift Clicking from the Crafting Guide) and Clicks a different recipe without using those items, any items picked up will be deleted.

Essentially, the rules to replicate this glitch are to try and shift-click any recipe that uses the items (such that the number of said items is between 1 and 63) dropped at the player's feet while the inventory is full, then shift-click another recipe. 

How to replicate (an example):

1. Make sure player is in survival
   1. ~ /gamemode survival
2. Fill the player's inventory with stone (except for two spaces)
   1. ~ /give <> stone 2176
3. Fill remaining player inventory with wood (with extra on the ground, but NOT exceeding a stack (64).)
   1. ~ /give <> oak_planks 160
      1. Any remaining items that exceeds the player's inventory capacity should expel out of the player in dropped-item form.
   2. At this point, you should have two stacks of "Oak Planks" in the inventory, and 32 x "Oak Planks" sitting below the player.
4. Make sure the player is standing on the dropped "Oak Planks" (such that, if an inventory space became available, the item would be picked-up by the player).
5. Open the player inventory. Have it so the Crafting Book/Guide is active and showing available crafting recipes (e.g. "Stone Button", "Crafting Table", "Oak Button", etc...). 
6. Shift Click any** recipe that uses the dropped item
   1. ~ Shift Click the "Oak Pressure Plate" recipe within the Crafting Guide menu 
   2. You should notice the partial stack of "Oak Planks" near the player will have been picked-up and is now sitting inside the player's inventory.
7. (Shift) Click any** other recipe (or the same recipe again).
   1. ~ Shift Click the "Crafting Table" recipe within the Crafting Guide menu
   2. The partial stack that was just picked up by the player will have been deleted.
      1. Additionally, the recipe just selected will have an abnormal distribution of items selected
   3. Sometimes, Shift clicking is not necessary for this step, a normal click works.
8. Items have been deleted, and do not reappear by leaving the GUI or re-logging.

Additional scenarios:

Replace "Oak Planks" with "String", and try Shift-Clicking "Wool" twice.

Replace "Oak Planks" with "Gold Ingot", and try Shift-Clicking "Golden Pressure Plate" twice.

Instead of two inventory slots with "Oak Planks" make it one (still with 32 additional "Oak Planks" at the player's feet). Try Shift-Clicking "Crafting Table" or "Oak Pressure Plate" twice in the Crafting Guide menu.

In a Crafting Table, try holding the ingredients for a Piston (with the rest of the inventory being filled with "Stone"), with 32 "Cobblestone" at your feet. Shift-Click the "Piston", then the "Chest". Sometimes, it will delete other items in the inventory instead (used in the recipe), and not the dropped item per-say.

In a Crafting Table, try holding the ingredients for a Piston (with the rest of the inventory being filled with "Stone"), with (32 x "Cobblestone", 32 x " ___ Planks", 32 x "Iron Ingot", and 32 x "Redstone") at the player's feet. Shift-Click the "Piston", then the "Chest". Several Items get deleted.

Additional information:

This bug only seems to work if the items being picked up (the items at the player's feet) amount to less than a stack.

The only items that are being crafted with seem to be deleted

This bug occurs in the Player Crafting Grid and the Crafting Table Grid.

The deleted items DO NOT reappear by re-logging.

**Shift Clicking on the same recipe twice DOES NOT CAUSE THIS bug IF the recipe maximizes the stack in the crafting grid for a singular item (e.g. "Oak Planks" to "Oak Button" – the crafting grid has 64 x "Oak Planks" ready to craft 64 x "Oak Buttons", but Shift Clicking it again will not delete the items (but Shift Clicking a different recipe will delete these items)).