Well since the issue is that it had wrong plugs... definatly not a warranty issue since the plugs are not the ones installed from the factory. As for waiving the diag fee, just because a car is under warranty, does not mean all repairs will be. Your cel can come on because you didn't tighten the cap. At the dealership I work at, all customers sign an hour authorized time for all cel concerns even if the car is under warranty. Sure you had already diagnosed the issue... but if warranty is to be done, then the tech must perform a diagnostic check themselves. Paying $100 for that if not under warranty is reasonable. Just buy the plugs, install them yourself and if the cel comes back on your good to go. Unless its proven the issue came from previous mods and no engine tune.