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.

I am very familiar with this type of damage.

It is usually racoons and they are just looking to move in.

I have had this on my own house.

You can do a te,porary patch with duct tape.

Fortunately it's an easy repair but it is probably not warranted and you will be charged to fix it.

Try to eliminate any access areas to keep the anoimals off of the roof, such as tree limbs.

The water that looks like it is coming out from the shingles may not actually be under the shingles.

You should be able to lift them and see if it is wet above.

I don't like the ponding at the gutter edge thoough.