I think we're saved mostly from really bad bugs by the strict instance equality check in ItemStack.isEmpty, but nonetheless this should be fixed.

You can see this happening by inserting the following code below the public ItemStack constructors:

private void E() {
    if (this.h && this == ItemStack.a) throw new AssertionError("TRAP"); // CraftBukkit
      this.h = false;
      this.h = this.isEmpty();
  }

And then right clicking a block with a sword.