It has a range of tools at its disposal to enable it to "crawl" your site and thus highlight technical problems, whether at the level of programming, the semantic field, duplicate content, internal phone number database meshing, broken links, the SiteMap or even the robot.txt file.
A good SEO agency should be able to give you the tools they use and will even be able, if you ask, to show you an excerpt or the entirety of an example of an SEO audit they have already carried out for one of their clients. Although there are free SEO audits online, an SEO agency will provide you with detailed and precise work in order to develop your digital marketing strategy.
I was talking to you about it in this video:

2.2. The programming skills of the SEO agency
A good SEO agency knows that the way a website is coded has a direct impact on its natural referencing.
Therefore, it must have in its team programmers (backend and frontend) who have been trained in SEO and who are therefore able to implement the recommendations of the audit carried out by the SEO expert in charge of your website. This criterion is, in our opinion, extremely important.