Did you change the FM? Maybe upgrade from step2 to step3?
I've tried a few FM myself for my son and some produces more bubbles than others when I shake the bottle to dissolve the FM. So far, Nestle NAN series produces the least bubbles and Similac (or Gain IQ) produces the most.
I think as long as the bottle is tilted correctly for her to drink, and not letting her drink the last 10ml will prevent her from getting too much air into her tummy. Otherwise, it should be fine. My boy was ok if I dont't let him drink the last 10ml of the FM in the bottle.