What is happening:

On a vanilla game/server, when the player joins, the "Special Recipes" (ie: recipes for dying leather armor, suspicious stews, tipped arrows, etc) are unlocked for the player. On a CB/Spigot server, these are not unlocked for the player. There is also no way for the player to unlock these (which makes sense, since in Vanilla they are unlocked automatically when the player joins) (note: These can be unlocked by a server operator but a player whom is playing the game is not able to unlock these recipes like how they unlock other recipes)

How we know this is happening:

I first noticed this in a plugin of mine, where the server's gamerule "doLimitedCrafting" is set to true. (This gamerule forces players to require recipes to be unlocked before they can craft an item). I noticed that I could not dye leather armor. 

After more and more research and testing, I found out this recipe is unlocked automatically on vanilla and not on CB/Spigot. 

When I join a Spigot server, I gave myself a crafting table and 64 leather. I crafted a leather tunic. Then I proceeded to pick up a flower, craft a dye with it and attempted to dye the armor with no avail. No item pops up in the crafting result.

When I join a vanilla server, I gave myself a crafting table and 64 leather. I crafted a leather tunic. Then I proceeded to pick up a flower, craft a dye with it and I was then able to dye my leather armor.

Another test I did:

When I join a vanilla server, if I type the command

/recipe give ShaneBee minecraft:armor_dye

I receive the error message "No new recipes were learned", if I do the same on a Spigot/CB server, the recipe is unlocked, thus proving that these recipes are not being unlocked by Spigot/CB when they should.

How this affects servers/players:

For the average server, this will make no difference, but this does in fact break the "doLimitedCrafting" gamerule, due to the fact if this gamerule is set, player's are locked out of crafting any of the "SpecialRecipe" items.

Testing Environment:

Craftbukkit server:

• CraftBukkit version git-Bukkit-ccd47a5

Spigot Server:

• CraftBukkit version git-Spigot-56f8471-ccd47a5

Same outcome on both Spigot and Craftbukkit servers