Small bubbles form on the surface of your crema when the coffee is very fresh (usually 1 - 3 days after roast day). The bubbles are caused by co2 gas given off by recently roasted coffee. This is the same gas which causes your sealed coffee to baloon in a sealed bag, the first few days after roast.
If you drink coffee too fresh (1 - 3 days after roast) it wont taste very nice. Some origins need longer to rest than others, but the general rule of thumb is to start drinking after 72 hrs from time of the roast and consume within 2 weeks or so. Some coffee tastes better after a week or more of rest... eg. some indian monsoon malabar.
If you see a few small bubbles in the crema, thats pretty normal. If the surface is absolutely covered in bubbles, then it might need another day of rest.