How to solve a roof vent leak?

Whats happening to my roof vent boots?
New roof two years ago. At that time the metal plumbing vent boots were replaced with rubber ones. Yesterday, while on the roof, I see that the rubber has been totally demolished by "critters" of some kind. Squirrels? Birds? Has anyone had this same experience, and is the roofing company liable for replacements?
GTB, thank you for your reply. The metal boots they discarded were effective for decades. The new ones less than two years. Thats the primary concern. I hope the lead or metal boots are still available, soybeans aint cuttin it.

Custom wedding gown
Custom bridesmaid dress
Custom mother's dress