Adding Super Users to Sites breaks theme

I have created a custom theme for our network of company websites and have discovered some odd behavior.

When I create a new site and add the super user to the site using the network dashboard, it breaks my theme. The Super User is listed as a user with no Roles.

If I go to the site and add the super user the theme is working perfectly.

The theme extensively uses short codes to provide custom style and content for the company website. It is only on those pages that the theme breaks.

I have fixed it by not adding the super user to the sub site I just thought it was a weird and unexpected outcome.