If your dough is in proper balance with regard to yeast level, and the temperature is not too high, the dough should not exhibit much of a tendency to bubble as you've described. A good dough temperature is 80 to 85F (probably favoring the 80F side). A dough that has too much yeastor one that is too warm will typically exhibit a greater tendency to bubble during storage in the fridge/cooler. Also, if you leave the dough rest at room temperature for an extended time prior to putting it into the fridge, this may increase the odds of having the dough bubble. If you put the dough into a plastic bowl in the fridge, be sure to leave it uncovered for the first 90-minutes or so, then cover it. This can also reduce the bubbling tendency. If all else fails, put the dough into a bread bag for refrigerated storage. Twist the open end of the bag to close it, and tuck the pony tail under the dough ball as you place it into the fridge, then kiss it good night. No need to leave anything open. Just be sure to oil the dough ball prior to dropping it into the bag, then just turn the dough ball out of the bag into a bowl of dusting flour and begin opening the dough ball into a dough/pizza skin, dress and bake. If the dough develops a bubble, I normally ignore it until I'm ready to use the dough, then just pop the bubble and open the dough ball.
Tom Lehmann/The Dough Doctor