If water hasn't got in from outside, the other big cause of corroded/wet-looking plugs is a failed coil pack or a leaking cam cover/rocker gasket letting oil or coolant creep down into the plug wells. If it's a coolant leak into a cylinder that would also explain a rough misfire, and it's worth them checking for a blown head gasket or leaking injector seals too - not just blaming the plugs themselves.
I'd push the dealer for a proper explanation of the actual root cause rather than accepting "plugs are worn so not warranty". If they can't say what let moisture/fluid in there, that's not really a customer-fault issue and worth escalating with VW customer care given it's been dealer serviced under an all-in plan the whole time.
