Could be caused by a module which doesn't provide a base path for a config entity, see for example:
Drupa8 - as a Symfony application - abstracts paths with routes. So paths may change, the route stays.
So the cited "The internal: scheme should be avoided except when processing actual user input that may or may not correspond to a Drupal route." means: If you can, use a route.
If you can not use routes, the right prefix for routed paths is internal:.