there are a few confirmed bad things about bubbles stones in marine aquaria, the most important three being{note this is my opinion that these are three the most important},
1they are inssufficient for aeration purposes,
2in a reef tank with proper flow the smaller bubbles tend to blow every where trapping pockets of gas under rock in hole in rock and so on, wich can lead to die off of air sensitave organisms in your tank.
3 the bubbles trap and carry protiens upward depositing them on the suface of the tank, reducing gas exchange.