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We don't refer to or use the EU laws here, everything we're entitled to is in British Law (SOGA, etc). As the contract is between yourself and the retailer, Apple are correct that you should be pursuing this with whoever sold you the phone.
Snag is, the EU regs aren't really a 2-year warranty in the way that is commonly reported on the net. The common suggestion that you have an automatic 2-year manufacturer/retailer warranty is, sadly, incorrect. 2 years is just a limitation period for making a claim against a retailer (in the EU), not a period where you're automatically entitled to a remedy.
What the EU 'warranty' is, and what your claim would be based around, is statutory consumer rights - basically that your item should be free from defects for a reasonable period. If the item doesn't conform to the conditions in SOGA, etc you can make a claim against the retailer.
If you think that the item has become faulty through no fault of your own and you should be entitled to compensation, you can contact whoever is responsible for Consumer Advice in your area for advice. You may need to demonstrate at some point why the item is indeed faulty (usually by way of an independent report) and you may need to prepare a Small Claims case.
Take the stuff in the 'This is Money' article with a pinch of salt, as with anything else from The Daily Mail!