wp_footer Scripts Using Wrong Directory

One of our clients websites is suddenly enqueuing the wp_footer javascript files in the directory of the current folder you’re visiting on the website instead of the root of the domain.

For example, if I’m visiting domain.com/sub-folder/ all of the scripts in the footer enqueue like this:

<script type='text/javascript' src='http://www.domain.com/sub-folder/wp-includes/js/admin-bar.min.js?ver=4.4'></script>
<script type='text/javascript' src='http://www.domain.com/sub-folder/wp-includes/js/jquery/ui/core.min.js?ver=1.11.4'></script>
<script type='text/javascript' src='http://www.domain.com/sub-folder/wp-includes/js/jquery/ui/widget.min.js?ver=1.11.4'></script>
<script type='text/javascript' src='http://www.domain.com/sub-folder/wp-includes/js/jquery/ui/mouse.min.js?ver=1.11.4'></script>
<script type='text/javascript' src='http://www.domain.com/sub-folder/wp-includes/js/jquery/ui/resizable.min.js?ver=1.11.4'></script>
<script type='text/javascript' src='http://www.domain.com/sub-folder/wp-includes/js/jquery/ui/draggable.min.js?ver=1.11.4'></script>
<script type='text/javascript' src='http://www.domain.com/sub-folder/wp-includes/js/jquery/ui/button.min.js?ver=1.11.4'></script>
<script type='text/javascript' src='http://www.domain.com/sub-folder/wp-includes/js/jquery/ui/position.min.js?ver=1.11.4'></script>
<script type='text/javascript' src='http://www.domain.com/sub-folder/wp-includes/js/jquery/ui/dialog.min.js?ver=1.11.4'></script>
<script type='text/javascript' src='http://www.domain.com/sub-folder/wp-includes/js/underscore.min.js?ver=1.6.0'></script>
<script type='text/javascript' src='http://www.domain.com/sub-folder/wp-includes/js/shortcode.min.js?ver=4.4'></script>
<script type='text/javascript' src='http://www.domain.com/sub-folder/wp-includes/js/backbone.min.js?ver=1.1.2'></script>

Has anyone seen anything like this before? I’ve looked all over for functions in the theme (custom built) but can’t figure this one out. Anyone have any ideas where to start looking?