2005 Hyundai Santa Fe CATALYTIC CONVERTOR

6 months ago, the "engine malfunction" light came on. My mechanic diagnosed the problem - said it needed coil assembly replaced and recommended I take car to dealer since it should be covered under warranty. Dealer said that the number 2 cylinder was misfiring due to spark plug leaks and replaced spark plug at no charge. Said it did not need coil assembly replaced. One month ago the malfunction light came on again. My mechanic could not find any problem and reset the light. About 10 days later, the car ran rough for a short period of time one day. This happened 2 more times over the next week or two (on rainy days when first starting in the morning). But then the car ran fine for about 2 weeks. Three days ago the car lost power while I was driving it (check engine light never came on as a warning). I had the car towed to my mechanic. He checked it and said that the catalytic convertors were clogged and that it should be covered under my Hyundai warranty. I had the car towed to a Hyundai dealer service dept. They ran a diagnostic test and said that the internal clogs in both convertors were due to the engine misfiring and therefore it was not covered by warranty. They also said that one of the coil assemblies was not original Hyundai part (although my mechanic never replaced a coil assembly) My question is: should I dispute their decision not to do the work under warranty?