Auto ads are designed to ignore all your CSS and insert the ads in a consistent way across different sites. There is no way to control the position or margins of auto ads.
If you want more control of your ads, then you should disable auto ads and use traditional ad placements. See Ad placement and how to create it - AdSense Help for instructions on how to ...
Although, not a primary ranking factor, we would recommend that you clean them up so there are no 404s or missing pages.
If an auditing software can detect these errors, then you can bet that Google can, too.