Hi
Siopao,
There is an acrylic plate near the bottom of the reservoir that should prevent most if not all of the air bubbles from getting sucked in by the pump.
Maybe reduce the speed of the pump a bit and see if it helps? I have two D5's in series (mostly for redundancy) and with them running at 40% the fountain effect is hardly causing any disturbance at all.
Maybe another part of your loop, like a radiator or a block is not completely air free as well, and is the cause of the micro bubbles you see going through. Depending on the complexity of the loop it can be hard work to deaerate it.
Is your reservoir completely sealed? Maybe there is a tiny leak somewhere and it is ingesting some air that way?
In the end, tiny bubbles can also be caused by cavitation in the loop itself (like from a pump). You can hear this as sort of a crackling noise.
If they are tiny I would not really get worried about them, I think you're fine as long as you don't have big pockets of air in your loop.
Kind regards,
Boris.