How do I add custom HTML to the content of an archive page’s posts?

I have a plugin with a custom post type for courses. I want to customize the content inside of the archive page’s posts and style it. I realize that the archive page is using the_content() to retrieve the posts’ content, and I’m able to use the corresponding filter to customize it; however, it’s stripping the HTML and not allowing me to style it. How do I get past this?

HTML comment cause issue in functions.php script root

I noticed HTML comment tag <!-- --> will cause issue on themes functions.php script if it is in the root of script(not inside a function).
I was working on my themes functions.php to add some Easy Digital Downloads action/filter, which i realized purchase button will continue to loading and doesnt add product to basket.
after clearing an html comment that was in the root of script,issue solved. i need to know whats wrong with having HTML comment in functions.php root ?