Are you sure your contractor didn't CUT any corners?
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.
When was the last time you were on your roof
"That new bathroom remodel was the best money we spent in a long time, I love the new tubs location"