Reseal the seals between the glass and the back portion of the tank, alot of people running the nano's get that problem where MB's come out due to vibration in the tank where the glass meets the plastic back. Are the microbubbles coming from the pump itself? Sit there and watch the return into the tank and see if you see any popping out.
and loosen up the spacing between the carbon (if you got it) in the second chamber or the sponge. Might just be up against the opening on the bottom preventing the flow to the 3rd chamber. had that problem when i had microbubbles in my jbj.
Edit: from what i read on nano-reef and all the forums for nano's, the major problems people have tht cause microbubbles is:
The seal between the glass and the plastic back, loose fitting on the tube from the pump to the return head, a crack or puncture in the tube itself, restriction in flow to the 3rd chamber (low water creates a whirlpool effect inside and pulls air into the pump). and the pump needs to be on the bottom of the 3rd chamber, specially in the 12g since its so small. pump might be too strong for it.