EU is telling Ireland to levy the general corporate tax in Ireland on Apple. Ireland has had that obligation all those years.

EU legislation on state aid has always been this way. It's a usual thing to force a company (Apple) to pay back government subsidies (incl tax subsidies) to a member state (Ireland), which says it doesn't want the money.

Member states granting illegal subsidies almost always say they believe the subsidies were legal or that no subsidies were granted.