It looks like there’s a missing " and > on the permalink and that line should be: <a>">

That said, your HTML is also malformed because you have an h3 tag directly inside your UL. Moving your UL item to after the <?php if ( $query->have_posts() ): ?> line and before the <?php while ( $query->have_posts() ): $query->the_post(); ?> line should fix the problem. You’re also missing the closing UL tag, but it could have just been missed when copy/pasting code here. You’d also need to move the closing UL tag to between the <?php endwhile; ?> <?php endif; ?> lines.

Here’s the corrected code:
https://pastebin.com/NUGSZ7Ba

<li class="medium-4 columns single_f_area">
  <strong><a href=""></strong>
    <div class="medium-12 columns thumb_image" style=" background:url(https://cuelearntest1.wpengine.com/wp-content/uploads/2017/05/53-6.jpg) no-repeat center; background-size:cover;">
      <h5>Behavioral Health in Primary Care (SIM Initiative)</h5>                                                                           
    </div>
    <h6 class="f_area_home_title">View Modules</h6>
  </a>
</li>

I suspect the link may not be in the custom control, but I’m at a loss as to what changed in WP to make this not work. Our test environment only has the WP upgrade and the problem exists there too. 4.7.6 works fine but 4.7.8 and forward is broken.