Hello, I have found this problem with potions:

When I create a potion using 

new ItemStack(Material.Potion, 1, data_value);

it creates the right Potion. So for example if I want to create a potion of regeneration, the data value will be 8193. And it works fine.

But the problem appears when I change for example the name of the potion

ItemMeta itemMeta = itemStack.getItemMeta();
itemMeta.setDisplayName(name);

Now, it will change the potion into uncraftable potion and there will not be any effect on it, it's color will also change to pink.

This bug is most probably present also for lore, enchantments and item flags.