Source code showing static and wordpress header in live site

Hi, I’m having trouble understanding why my website is showing the header twice and not the footer. I first uploaded a static version to my remote server of my site, and then overwrote it with my WordPress version. The css and js are still being read from the static version at the root of my public_html but the posts and their content are dynamically displayed from worpdress version. I think I may have update certain links upon migration but not others but im not sure where to look to change the rest?

So its one page made up of 3 php blocks.
<?php include ‘header.php’; ?>
<?php include ‘index.php’; ?>
<?php include ‘footer.php’; ?>

This is not a php question, its just there for reference.