In order to get all of the submodules, the git plugin looks in the local configuration file:
However, the .git/config file is local per repository, and old entries and sections do not get overriden. Therefore, when a submodule is no longer in use or has moved, the old configuration can cause an error. Anyway, the local configuration is not part of the remote repository, which is the correct clean repo which is the exclusive authority on git configs.
A possible solution would be to call deninit in order to remove the old configuration.