Correct procedure to thaw frozen pizza dough?
Thawing frozen pizza dough should be done overnight in the fridge, but allowing it to come to room temperature is not strictly necessary, because it will be cooked in a relatively hot oven in a short time. In fact, cold dough is often easier to work with. 
However, 3 hours sounds like a lot for pizza dough, which may caused you to overproof it.

No, it does not make much of a difference if your container was opened.

Bubbles tell you that the yeast in your dough is active, which is often a problem with frozen dough. If you don't have bubbles, the dough will seem dense and undercooked even after baking for a long time. So bubbles are a good sign.