Then that's Ireland's problem, because Ireland was the one who let Apple get away with the lower tax rates in the first place. Nobody forced the Irish government into doing so, they likely thought that the benefits of attracting so many multinational companies outweighed the drawbacks of collecting lesser tax revenue.
So after all these years of having multinational companies operate in their company, now they try to get the tax revenue back. Notwithstanding the possibility that had the higher tax rate been in place from day one, Apple may very well have opted to not set up shop in Ireland.
Get Ireland to cough up the missing tax dollars, not Apple.
Apple them selves said no special deal was made, so they had to pay 12.5% according to that. 0.005% is not 12.5%.