Strange roof damage

We had a new roof installed on our house last year, but it has started leaking recently. As can be seen in the linked pictures (https://photos.app.goo.gl/uo4sUx7LagGZw3Py8) there is a hole in the rubber cover over the bay window which our contractor claims was chewed by some animals. I find this explanation somewhat strange since animals usually start chewing at the edges, not in the middle of a flat surface.

Anyone familiar with this kind of damage ?

Another puzzling, at least to me, detail is water sipping from under the shingles long after the rain stopped.

Thank you in advance for you comments and advice.