They won't impact on the integrity, but will be noticeable and will not go away. Have them come back and sand them with steel wool and re-treat.

Also ask them how many coats were done, and what the drying time was between coats.... And what is recommended by the manufacturer.

What type of finish did they use? A buff n coat is probably the solution but cant say for sure without seeing the floor. Also if they will be using a water bourne urethane DO NOT USE STEEL WOOL!

Thanks everyone.

They used a Zinsser Sealer Shellac/water, Poloplaz Supreme Polyurethane - 2 coats. The flooring had flaws from sanding and they resanded and repeated the process.

The flooring contractor was already unhappy that I had him redo the floors because of the significant dents and waves from the uneven sanding in two rooms. All of the floors had a rough texture after he was done the first time and you could see and feel the rough grain and in some spots felt like the finish was almost bare. His response to me was that I could put rugs to cover it the uneven sanding. No deal!

So with an attitude, he said he would resand the two rooms that were sanded unevenly and screen and recoat the other rooms to help with the rough grain. He did all that. The grain no longer feels rough but does not look smooth like they did before they were refinished. He never admitted to me that he thought there was a problem but did admit to my GC that the work was not done correctly by his crew.

During this process we were out another 7 days in a hotel (getting expensive here). So, I decided when we came back for the walk through, unless there significant flaws I was just going to love everything and move forward. I didn't see the bubbles until a few hours after the very brief walk-through. I cannot see living with those as they are significant through out the two rooms they resanded. I do not see them in the other rooms where there was just screen and coat.

The reason for refinishing the floors is because of a flood we had in the kitchen and a small portion of two other rooms requiring a small portion of each those rooms to have some flooring replaced. At the same time we decided to do a full kitchen remodel as we had plans to do this within the next five years so thought it would be prudent to move up our plans.

The GC is having him come back Monday to look at the bubbles.

Now, I have to say, this flooring contractor was by far the most expensive bid and has had a very good reputation in the community for over 28 years (why we selected him over cheaper bids).

This is where your GC earns his pay: it's his job to fight with the flooring guy, not yours.