Don, Sometimes air bubbles seem to appear "for no understood reason," which is related, as Jennifer mentions, to temperature differences between materials, and possibly a kind of "reaction" as adhesive dries.
The best way to keep this to a minimum is to be sure that you roll the floor very consistently working outward from one starting point, and always towards outer edges. Once the floor has been put down, you often need to check for small bubbles beginning to appear 20-30 minutes later, and carefully "chase" them to an edge with the roller.
If the floor has down less than about 48 hours and the glue did transfer to both surfaces originally, you still have a good chance of sticking them back down. First, try the weight method LJ suggests, next by making a small puncture at one edge of the bubble (for air to escape) and rolling the air out.