Do you have a skimmer? If you do then there's your bubbles. As far as having bubbles in the main tank, IME they don't hurt anything at all, you might get some sliming off some corals but nothing major, IME.
FWIW, I inject bubbles at least 3x's a week in my main tank's water column by putting a 1/4" on the return pump's intake. I usually do this when i turkey baste my rocks and I have all that gunk flying through the tank, thus making the tank itself a protein skimmer
of sorts. The gunk is rises with bubbles, gets picked up by the overflow and dumped in the skimmer chamber to be exported. This method is advocated by lrdhawke , whom I'm not sure if he posts here or not, the main difference between my application and his is that he actually does it everyday with a pump that's on a timer. The model behind this is trying to "replicate" the effect of waves on a reef, where a lot of bubbles can be seen due to the waves crashing on it. HTH