I read the posts below and they were informative. The problem I am having is how many bubbles are acceptable? We had our floors down about ten years ago and I don't remember any bubbles. We just had them redone and there are enough to be noticeable. It's true that you have to see them in certain light, at a certain angle. I realize once the furniture and area rugs are back in it won't be as noticeable, but does that make it ok? The same guy did the floors ten years ago and said he uses a different product now and that is why there are these little bumps now that weren't there last time. He said the product he use to use is no longer legal here in NJ. He came back and buffed the floor and put another coat of poly on once and the floor is better. I don't know if he were to do it again how much it would help? I don't know if we're being to picky? Some of the bumps/bubbles a very small and some are a bit larger, and he said, as the post below states, that they "will walk off".

When the finish is applied cover windows with old news paper. Light is a funny thing it bakes the floor causing bubbles. Or the finish is not good quality. Good Luck

Are they held suspended in the finish, or are they popped craters on the surface/fisheyes?

Several points, it may be that 10 years ago you were not as discerning as now. Most site applied finishes will have some minor flaws that werent noticeable before all the world started using pre-finished products to compare with. A machine applied finish, done in a controlled environment will be smoother than a site finished application (I can hear my comrades rattling sabres at me already, lol)
Also, as a finish matures, the act of walking on it, and general maintenance, will remove most small blemishes over time. A 3 year old finish will thus be smoother than when it was first applied.

If the extra coat that was applied to your floor removed the most offensive of the bubbles and blemishes, I suggest accepting the coat as a bonus, and allow time to heal what remains.

The suggestion about putting newspaper up is an excellent way to prevent the little craters but needs to be done before the finish application.