Bukkit

This info was mainly taken from https://minecraft.gamepedia.com/Recipe#crafting_special_.2A

 There are some special dynamic recipes outside the scope of this plugin that performs item metadata manipulations (nbt tags). So the normal recipes are unable to handle the associated data specified below

Item repair

 Destroyable Items can be quickly repaired by putting 2 similar worn items in crafting grid (2x2 or 3x3, shapeless, or grindstone) and the resulting one will have combined durability +5% (i always use this!)

 However normal recipes are unable to calculate enchantments data so they will be lost, to preserve them repair the item with an anvil instead

Pattern design and duplication for Banners and Shields

 Normal recipes are unable to handle pattern layers data

Fireworks rockets, stars and fades

 Normal recipes are unable to handle the wide range of combined visual effects data

Potions, Tipped arrows and Suspicious stew

 Normal recipes are unable to handle the attached status effects data

Dyeing Shulker box and Leather armor

 Normal recipes are unable to handle multiple color information data

Map cloning and zooming

 Normal recipes are unable to handle additional bitmap image and coords data

Book cloning

 Normal recipes are unable to handle the contained text data