This is not an issue with the theme but your URL or permalink setup. You should not add child pages to your home page because that is already the first bit in the URL. In your case, alternate-homepage is the same as hunterprograms.com so there is no point in making child pages of it as it is the main page of your site or the parent of everything in your site. If you add child pages to your home page, WordPress (not the theme) will add the parent slug to the URL like what you encountered.
Regarding SEO, no, it will not hurt your SEO. In fact, setting child pages to your home page will hurt as the page slug has no meaning alternate-homepage/hpes-guidance/. I can’t go deeper with regards to SEO as this is outside the world of themes. Please see this article for guidance. Or, it would be best you consult with a SEO agency.
Thanks.