2008 Hyundai i30 rattling

I haven't had any real issues with my 2008 Hyundai i30 diesel until the last 18 months to two years when I have had it back to the dealer numerous times for a fairly consistent puff of smoke and a "can of marbles" rattle for five or so minutes on the first start for the day. First it was the turbocharger, then injector seals, but that didn't fix it, now they say they have found metallic shavings in the injector pump and that it would need replacing along with the fuel rail, lines, injectors etc, and that it would be a warranty repair and that they had done this repair a fair few times and not to worry. But Hyundai knocked back warranty claim on the grounds of "contaminated fuel". I think it is faulty pump. Your advice would be much appreciated.