Foam brushes are nice because they're disposable, but they do leave bubbles, especially in poly.
If you are using a regular brush (and it's a good one that's designed for applying poly), make sure you are NOT shaking the can of poly to blend it. Use a stir stick very gently so you don't introduce bubbles into the product.
If you are not doing either of the above, perhaps Moderator Steve (or one of the other professional painters on this site) will have another idea. Let us know.