Someone told me that you can't do this, due to expansion and moisture issues - that the parquet floor has to be removed. Is this true?

I have sanded and refinished my upstairs wood floors and both rooms (done at seperate times) have bubbles on them. I stir very easily, poor very slowly, use a lambs wool applicator to put it on with. I lightly sand with 180 or 200 grit (I can't remember which) between the first and second and second and third coats, which smooths out the bubbles. The third coat is my problem. I dip the lambs wool applicator very carefully, but the bubbles are coming from the back and forth motion of me putting it on the floor. I am going to be doing this to my downstairs living room and hallway this weekend, and another 2 bedroom in the immediate future. Any Ideas what I am doing wrong here. I am using a polyurathane from home depot as well as there 4 disc orbital sander, which might I add is leaving small swirl marks on the floor. My floors don't have much of a previous coat, so a drum sander would probably make it worse, due to digging in. You can't see them unless you are on your hands and knees, but for a wanna be perfectionist that knows nothing about this. Yet my wife wants the whole house done this way. It is an eyesore for me. I use 3 different grits on the orbital going down to a real fine grit. The bubbles are my main concern though. Any suggestions. Thanks