Theme trying to load some assets from multisite main site url

We have a Multisite set up and one of the sites has its own theme. However the design is not working, this is because some of the CSS files are not being called.

On investigation it seems that some css/js files are loading from the site url, but some are trying to load from the url of the Multisite admin/main site, which is proxied and behind a firewall, thus not available externally.

Any idea how I can get all the theme assetts to load from the same url? Why would they be loading from two different urls?

Example code below.

<link rel="pingback" href="" />
<link rel='stylesheet' id='theme-bootstrap-css'  href='//' type='text/css' media='all' />
<link rel='stylesheet' id='theme-style-css'  href='//' type='text/css' media='all' />
<script type='text/javascript' src=''></script>
<script type='text/javascript' src=''></script>
<script type='text/javascript' src='//'></script>
<script type='text/javascript' src='//'></script>
<link rel='' href='' />
<link rel="EditURI" type="application/rsd+xml" title="RSD" href="" />
<link rel="wlwmanifest" type="application/wlwmanifest+xml" href="" />
<script>window.wpJQuery = window.jQuery;</script><link rel="alternate" href="" hreflang="en" />
<link rel="alternate" href="" hreflang="cy" />