I stumbled upon this error after removing a block type 'logo_listing':
RuntimeException: Adding non-existent permissions to a role is not allowed. The incorrect permissions are "create logo_listing block content", "delete any logo_listing block content", "update any logo_listing block content". in Drupal\user\Entity\Role->calculateDependencies() (line 207 of core/modules/user/src/Entity/Role.php).
Solution
For some reason the system was thinking the user still had these permission, while they were not found in the database.
- export your current config (drush cex)
- In your config folder, search for the permission
- In my case it was stated in user.role.content_editor.yml
- remove every line that holds permission of this block type
- import your config
Now the error disappeared!