Roof work isn't quite the monster on these things that it's made out to be. Your best bet is probably to try and Identify what is sticking up. (Screw, piece of flashing, etc.) Once you know what your dealing with you can probably figure out a way to fix/remove. It doesn't sound like something that would likely be covered by warranty unless it's due to negligent craftmanship.
Cut it 3 times and it's still too short...
2017 Sandpiper 381RBOK
2006 Ram 3500 Cummins Dually