That is what happens with a lot of international IP income and not just Apple.
What is happening in Ireland today is that the EU "rules" are being applied retrospectively to legally paid and audited tax returns.Ireland didn't set a special rate, they just allowed jurisdictional rules to apply which meant that Apple could take advantage of lax Irish laws.
The EU has decided that the durisdiction didn't apply and are demanding tax based on their ruling going back a decade.
For those who don't know, the smash and grab by Brown on contractors used the same retrospective taxation. Every single case that came to court was defeated because it is illegal under UK and international law.
I expect the EU courts to uphold this travesty, therefore crippling the Irish technology industries causing an exodus seen in Silicon glen.