I have a business website that is coded purely in HTML/CSS/JS. I also made a blog section and used WordPress for it.
example.com : is HTML, CSS, JSexample.com/blog : is WordPress.Does this make some issues for SEO? Because WordPress creates its own sitemap.xml, own .htaccess, rel canonical is example.com/blog and etc.
What's your suggestion in these situations?
You can submit different sitemaps in Google Search Console. This way you can have your root directory sitemap.xml and then have a separate one for the blog directory.
Having blog in the subdirectory or in a subdomain is one of the most debatable topics in SEO world. As per my experiences, studies and experts opinion, I'll say that there's no problem having blog in your subdirectory. Instead, it'll help your SEO as google will consider it as a part of your main website. (Subdomain offen treats as different website). And you can have multiple sitemaps and can submit multiple sitemaps for one website. If you see google's guideline, google also suggest to submit sitemap individually for links, images, videos etc. Hope that answers your query.
.htaccessis per directory, so not problematic at all. Nor is it visible to search engines directly. It just controls how the server works. So as long as the server is working fine and Google can crawl, no worries there.