If you want to run Disk Utility First Aid, then run it on the hidden Container (it will automatically scan all APFS volumes within that Container as well). Within Disk Utility you may need to click "View" and select "Show All Devices" before the hidden Container appears on the left pane of Disk Utility. Even if the First Aid summary says everything is "Ok", then click "Show Details" and scroll back through the report to see if any unfixed errors exist. If there are errors, then run First Aid again until they are gone. If after several attempts the errors remain, then you will need to run First Aid while booted into Recovery Mode.