Do they make it back to the main tank or do you have bubble traps/baffles? The main reason I don't like bubbles in the main tank is because they irritate the corals and make them close up.
I have lots of bubbles in my sump, but by the time it gets through bubble traps and all the cheato/macro it's clear water going back in. Another cause of micro bubbles in the main tank is how much of a 'water fall' you have in the last baffle going into the return section. If it's gentle, I get less bubbles if any. If the level in my return section is down and the water flows over, I get the bubbles.
Hope that helped,
Tom