I was looking for not-deprecated way to apply itemstack data for long time and found bug. When you actually trying to change durability now, it changes itemstack data instead. Ex:

ItemStack item = new ItemStack( Material.INK_SACK, 1 );
item.setDurability( (byte)13 );
(This will be pink dye.)

And i tried to apply item data like this, but it didn't worked too(got default item):
ItemStack item = new ItemStack( Material.INK_SACK, 1 );
Dye dye = new Dye();
dye.setColor( DyeColor.GREEN );
item.setData( dye );