This is just a fact of life, things don't last forever. This plumbing vent boot has sercombe to the elements. If caught in time it could be a fairly cheap repair. If not get ready to replace your roof.
"That new bathroom remodel was the best money we spent in a long time, I love the new tubs location"
When was the last time you were on your roof
Are you sure your contractor didn't CUT any corners?