We had the same thing happen to our Jay Flight. It was actually some of the plywood "splintering" upwards. Jayco stepped up and allowed for the entire roof to be replaced under warranty, and there was only two very small spots. Jayco has a true two year warranty and I had three months left on it. I was VERY surprised they signed off on it.
However, if your unit is passed it's one year warranty by Keystone it sounds like your on your own. The longer warranty on the roof by the manufacture is just for the rubber membrane itself.
I would cut it, fix what's sticking up and patch with Enternabond. Even with mine being under warranty I still had to think long and hard about letting them replace it for something so minor. It all depends on your dealer.
2018 Ram 3500 DRW CCLB Aisin 4.10 4x4
2018 Jayco Talon 413T
B&W Companion