are you using soapy water?
If you are, make sure your not stirring up the water with the soap, its gives it a ton of micro air bubbles that find its way on your finger and on the film. It should work its way out in a couple of days, but sometimes alittle too much soap prevents that. How long has it been? I put a BSE on my iPod a few years back, took about a week for it to settle.
is there a speck of dust underneath causing the bubble? try doing it in the bathroom after a nice hot shower. The humidity in the air will keep the dust down to a minimum.
Ive put on a dozen or so different protectors in the years, wet and dry installs. I never had a real problem with air bubbles. Just take your time, pay attention to the water and air bubbles...use as little water as you can.