Sanding them should remove them or sand a little and recoat then sand some more.

 To prevent them apply the epoxy when temps are falling such the late afternoon, early evening.  Not in the morning or early afternoon.

useing a slow hardener will help also. any time you speed the cure time you create a place to trap someting,or push the temperature 

Had the same thing happen to me last night,  I am using a slow hardener and applied expoxy to the deck using a roller,  I used a heavy duty shop towel to wipe down the deck while the epoxy was still curing and the bubbles are gone.  Deck looks great this morning expect to the 2 skeeters that like to die in curing expoxy.