My Aqua C Remora Skimmer has always spewed large amounts of microbubbles out of it along with my Maxi Jet Powerheads. I havent seen any negative effect on my corals or fish. You will be fine. If it bothers you alot, try adding a small sponge where the water comes out back into your tank. That may catch some of the bubbles. If your aquarium is new or your filter is new it may just need a little time to break in and get used to being used.
Just avoid airstones and bubble walls. These types of bubbles can get caught in fish gills, potentially hurting or killing them. Also when the bubbles pop at the surface, you will get alot of saltcreep.
Hope this helps.