When it comes to SEO it’s important to remember that the search engines look at all aspects of your website when determining rank. A website may look beautiful and be easy to navigate, which is important from a user perspective, but what’s going on on the outside of the site doesn’t always accurately reflect what’s going on on the back end of the site which is really what the search engine spiders are seeing. If you’ve incurred a penalty, you will obviously need to conduct a technical SEO audit to figure out what went wrong but it’s recommended to conduct an audit on a regular basis to try and prevent a penalty from happening in the first place.