Apple, like other european giants, sends all its European business through Ireland, which is a convenient tax haven. Now, Ireland seems no longer happy being the tax haven, and Apple is forced to pay somewhat normal taxes.
Ireland is happy to be a tax haven and would like to continue being one - the magic phrase is "put on the green jersey" (and think of the nation's economic interest rather than demand fiscal transparency from Apple)
But the EU isn't happy for Ireland to be one, and has forced it to close its dodgiest schemes as it also did with the Netherlands.
Also, the EU hasn't said Ireland is a tax haven, it said it's a tax "black hole"