If you could take a picture it might help us understand your problem. Are you saying that it is in a block or two?
Sometime pressing with steam will help remove it. OR it could be that the bubble area is larger piece than the fabric next to it. That might mean un-sewing and resewing. OR you might be able to finish the top and when you pin and quilt it (or take to the quilter) the 'bubbles' might stretched out and quilted out . . . but that is a guess and golly at this point (and cross your fingers). It all comes down to how 'perfect' you want the quilt or how much it troubles you.