Micro-bubbles can be a pain in the butt as there can be many causes for them.
Did you maybe bump something between your return pump and return line? Sometimes a leak around a fitting will allow air to enter the water flowing through the lines. Due to the speed of the water flowing through the return, a vacuum is created and air is sucked into some of these small leaks rather than water expelled out.
Kind of like how air is pulled through those weird vacuum nozzles on the end of sinks in chemistry laboratories in school.