Hello and thank you for your inquiry.
I would suggest putting the filter pad back in and clean/replace it often as that will help trap the bubbles and not allow them to get pulled into the pump and back into the tank. I don't believe the live rock is causing the microbubbles (you would probably get the same with the bioballs), but the water "splashing" in to the filter chamber is creating bubbles that are being pulled through. The filter pad should help eliminate these.
No the microbubbles shouldn't harm any marine life in the tank, but can sometimes cause corals to get irritated and not open fully.
If there is anything else we can do for you please let us know.
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