So, poor behaviour is fine, as long as you weren't stopped before you started doing it?
Europe did do something about it, at the speed of international government agreements. You can't honestly be expecting that kind of organization to pre-empt every kind of misbehavior and favoritism inside its member countries.
Ireland and Apple weren't following the law, that's the whole point of this.
That makes it seem like the EU decided Ireland's corporate tax rates were too low but that's not what happened here. Ireland gave specific tax considerations to Apple that it didn't give other companies which is illegal in the EU. This is just forcing Apple to compete on a level (tax) playing field with other corporations.
They can't. The world is uncertain. Sovereign Nations legally have the power to do anything they fucking want in the regions they govern (they might be restricted by their own laws and constitution, but it is an internal one).
In this case, it appears that Apple abused certain Irish tax laws to an extreme degree. The EU is well within its rights to punish Apple for doing so.
Corporation Tax in Ireland is 12.5%. Europe is insisting only that Ireland actually collects it. If, as alleged, someone in Fianna Fail made a deal with Apple thirty years ago to charge it, and it alone, a different rate? It's not on the statute book, the power to do that is not included in law, and therefore it's Not A Thing. Oh, and also someone committed a serious crime, but it's Ireland and they'll never be prosecuted.
It is one thing to change the interpretation and use that going forward. Completely different to change the interpretation and apply it retroactively.