The reason is that its not showing up
<?php if ( has_post_thumbnail() ) : ?>
<a href="https://wordpress.stackexchange.com/questions/206672/<?php the_permalink(); ?>">
<?php the_post_thumbnail(); ?>
</a>
<?php endif; ?>
You are displaying just a link with check that is featured image exists or not
It seems, your post doesn’t have featured image, select any featured image or just remove that check from it, as i can’t see any need of it.
So your code will be :
<?php get_header(); ?>
<div id="main">
<?php if (have_posts()) : while (have_posts()) : the_post(); ?>
<div <?php post_class() ?> id="post-<?php the_ID(); ?>">
<a href="https://wordpress.stackexchange.com/questions/206672/<?php the_permalink(); ?>">
<?php the_post_thumbnail(); ?>
</a>
</div>
<?php endwhile; ?>
<?php include (TEMPLATEPATH . '/inc/nav.php' ); ?>
<?php else : ?>
<h2>Not Found</h2>
<?php endif; ?>
</div><!--Main End-->
<?php get_footer(); ?>