Don't know what finish your contractor used, but roughness on a finished floor is usually due to not cutting down grain raise in those areas.

Discuss this with your contractor.

I would guess that there's something in the finish in those areas. Consult with your floor finisher. If the rough areas look good and the balance of the floor generally looks good, it might be best to leave it alone. Finish application is impossible to get 100% perfect. In trying the improve these areas, you might end up with a worse problem. Poly is hard to do spot touchups on.

Thank you for the replies. I am having a really hard time over this one. I have never complained about any job anyone has done before. One of the spots is about the size of a tea cup plate but you can see it from across the room. The other area looks fine but it feels terrible and is a BIG area. If I were to walk over it in nylons I think they would pull. My fear is that while the larger area looks fine that over time this area will collect dirt in all those rough ridges and look terrible. If is was only the small spot I would not say anything because I am putting a rug there anyway. The spot in front of my pantry is going to high traffic. Its in the middle of my newly remodeled kitchen and it feels bad. I am so afraid to say anything because I don't want to make any other areas that look fine worse and it is a poly finish.

It is a conundrum. I can't count how many times I've faced the same dilemma.
We've had pretty good luck in similar instances lightly hand scraping the rough area, sanding it with fine grit sandpaper then applying Minwax spray polyurethane. We usually have to use the next shinier product (i.e. if the floor is sating, we use semi gloss) and it takes a knack to get it just right but it works better than trying to brush on a coat of poly.