I'm not familiar with that skimmer, but it sounds like it needs to be adjusted. Bubbles should only be going into the pre-collection chamber.
Micro bubbles aren't usually harmful, but they can cause massive salt creep. I read somewhere that too high a concentration of micro bubbles can interfere with a fish's slime coat, but don't recall how, or where I read that so take it with a grain of sea salt.
Someone stop me! Please! But... not just yet...
55 Gal Tropical FW
55 Gal Mixed Reef