roots under old liner?

i'm going to help my daughter replace their inground pool liner. when we pulled the old liner out, there were some small roots under the liner,like webs, on one side of the bottom. it's the vermiculite type bottom. what do you suggest we do to fix this problem before installing the new liner. this old one was there for 20yrs. is it smart to tear the roots off flush ?, and what about using some kind of weed killer on the side of the bottom where these are, would this stuff have any adverse effect on the new liner? thanks Randy