Thanks for the advice. I will definitely try to get the contractor to fix it. There is another area near the ones I cleaned that has to be removed and replaced because he didn't level the concrete foundation and apparently the boards aren't sticking to anything but air. They are "soft" when you walk on them. Perhaps he will do the others at the same time, but he was not very good to deal with the first few times around and couldn't understand why we wanted all the putty and glue removed. We still have the stuff all over the place but mostly you can only see it when the light hits a certain way. Still, it keeps me from getting the shine I was hoping for with the wood floors and they always look dirty.
Thanks again. As a result of your post, I don't feel as badly as I did yesterday! Will keep you posted. Also, will try to take a picture tomorrow and post a link, if the damage if visible.