You could have bubbles if the filter is pulling water more quickly than the system can refill, so if you fill the water just a little higher, it may help. Otherwise, you could have a lid not quite tight enough on the pump, or a plug that is loose. Tighten all the fittings, make sure the water is high enough, and then let it run for a while (an hour) and see if it clears itself up.
A few bubbles are fine, more than that or large amounts of air that make the pump chug or gurgle are not okay for running the pump…