According to press release, the scheme could be legal according to some Irish laws, but it violated EU law, which also applies to Ireland as a member of treaty. If government of Ireland didn't take EU law in account when applied tax rulings, that doesn't mean it was acting legally. So it more looks like the tax office lost your tax declaration and you decided you have your own personal tax rate of 0. No surprise, when the declaration will be found you'll be charged.