Missing or Invalid Theme Error

Hi @craigkendall, thanks for reporting this.

Downloading themes (or modules) by Composer doesn't automatically install them. And removing themes by Composer doesn't automatically uninstall them from Drupal as well.
What put these themes to core.extension is not a Composer but Install (or Install and set as default) action on the Appearance page (or enabling theme by Drush).
To get rid of unnecessary themes you have to do Uninstall action on the Appearance page (or do it by Drush) before removing the theme by Composer.
The same way as any other theme, by the way.

But you are absolutely right regarding material_stable9, this theme is hidden and can't be uninstalled from the Appearance page. To uninstall this theme you either have to remove hidden: true property from material_base/themes/material_stable9/material_stable9.info.yml to make it visible on the Appearance page or uninstall it by Drush: drush theme-uninstall material_stable9. This bit is not yet documented anywhere because I still have doubts regarding using own instance of the Stable 9 theme, it may be subject to change.

You are of course correct. Thanks! Issue resolved.