Sorry to wake an old post however I came across this thread and I thought I could contribute.
To the OP's original question, "Has ANYONE EVER had warranty work denied by Ford?" My answer is ABSOLUTELY!
I have a 2017 Lincoln MKZ 3.0 TT Black Label. I am not the original owner. I bought the car with just over 52k miles on it. That means the 4/50k bumper to bumper was expired however the 6/70k powertrain warranty still applies. For those who don't know the manufacturer warrant follows the vehicle not the owner.
I was driving the car and check engine light came on and it was running rough. I pulled over and checked the codes (I carry a OBDII scanner with me). I got P0302 and P0305 (misfire on cylinder 2 and 5. I reset the codes to see how quickly they would come back. Fairly quickly the check engine came back on and P0305 was the fault.
I took the car to the a Ford Dealer (Lincoln dealers are further and more rare). Initially asked for the repairs required for the misfiring and "the works" oil change and service.
They pulled the cylinder 5 spark plug and the side electrode was mostly gone, the plug appears to be to be blackened don't know if it was cleaned at all but still has an oily sheen on it (obtained from dealer later). I had to wait a day for them to get tooling to pressure test the cylinder and then another day because the tech called out. Basically they found not compression on cylinder #5. They borescoped the cylinder and found metal pieces (likely from the plug electrode) and scoring of the cylinder.
They called to tell me I need a new engine, good news it would be covered under my powertrain warranty. They just needed to submit the parts list, but they did say they really didn't have the time or ability to do that work but the service tech was like, "but you didn't know that, I probably would have told you had I known". Keep in mind the appointment to drop off the car was booked online which they apparently say doesnt work but they would check it out anyway....because again as the service tech says, "you wouldn't have known that".
Anyway, long story shortened, the factory representative tells them if the spark plug caused the failure it is a maintenance item and therefore isn't under warranty. The dealer call to tell me and gave me the Ford Customer service number which I called. Spoke to a rep who had to look into the issue. Came back and said the same thing and when I said there is no way that they know for certain that the spark plug caused this, they don't know what caused the PLUG to fail. They said they would have Engineering evaluate it and days later I get the same result, the plug failed and therefore it is not covered under warranty.
They never inspected the other plugs, never pulled the heads to look for any other issues (didn't even ask as an option which I would have paid to have done). Also these are the factory plugs the mileage is just over 57k and first plug replacement by the manual is 100k. My take is the plug failed due to some other issue. However they are denying my warranty. So yes, it does happen and I am working to fight it but options are limited and the cost out of pocket goes up.
This is current and ongoing so still working through it. Hope that answers the questions and maybe someone else out there has seen this or finds this in a search.