Omega preprocessing functions are sometimes called on admin pages when using an admin theme

I'm experiencing the same thing as Adirael in comment #3 on https://www.drupal.org/node/2229867 so I'm creating a separate issue for it. Quote from the comment:

I get a "Call to undefined function omega_layout()" when trying to enter the administration pages. That's fixed if I clear caches but it comes back at random and get's fixed only if I clear caches (using drush).

The version that Adirael used at the time was Omega v4.2 but I'm seeing the same problem with v4.4.

Here's how to reproduce this error:
1. Install Omega and make a subtheme that you enable and use as a default theme.
2. Add Seven as an admin theme
3. Run drush cc all
4. Go to a public page where the omega subtheme is active as the first page you go to after flushing the cache
5. Now go to an admin page where Seven is supposed to be used. The error should appear.

In theme() when the theme registry is fetched on the line "$hooks = theme_get_registry(FALSE);", the omega preprocessing functions are present among the page preprocessing functions. When it works as it should, they are not present there so I think that's the problem.