What kind of pump do you have? Can you update your signature please with all of your pool and equipment info? Also, did you lube those o-rings with silicone? When was the last time you cleaned the filter?
Just make sure that grease isn't petroleum-based. Silicone lube is best for the rubber. My pump always has as few of those bubbles as well. I drove myself nuts trying to eliminate them completely checking all valves and fittings before the pump for a suction air leak. I know we would like for it to be perfectly clear of all air 100% of the time, but each pool is different. I usually do like you and kick it up to high briefly each day to purge them. As long as the water level doesn't drop significantly or you lose prime you should be fine. If you wish to pursue things further, checkout the link below.
If the grease you used is oil-based, then that's bad. You need to clean that off thoroughly, from o-ring and from the two channels it sits in, and then use the right stuff. Here's the hows and whys of it:
My pump lid has the same ridges. There are always a few bubbles in it. Unless they get worse and actually build up over pump runtime, you can ignore them. I don't even know if mine go away eventually or not. Non-issue.