When a CraftItemStack is internally generated from a NMS ItemStack with a tag of "Damage: 0" (Damageable things in the inventory (sometimes?) have that tag) - it will have an empty ItemMeta (hasItemMeta() == true), Bukkit ItemStacks of damageable items do not have an item meta (if the item is not damaged) (hasItemMeta() == false), so isSimilar will return false.

Reproduction: get the players Inventory and getItem() on some slot with a undamaged damageable item. check .isSimilar() with a new created bukkit itemstack 

@EventHandler(priority = EventPriority.NORMAL)
public void onJoin(PlayerJoinEvent e) {
  ItemStack shears = new ItemStack(Material.SHEARS);
  e.getPlayer().getInventory().setItem(1, shears);
  System.out.println(e.getPlayer().getInventory().getItem(1).isSimilar(shears));
}

Suggested fix: hasItemMeta() should return false if there is just a single tag of "Damage: 0" and nothing else.

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