Are you certain that your git version supports submodules? You didn't mention the version of command line git you're using, so we can't tell if it is supported by the plugin. The plugin needs at least 1.7.10, and is better with even newer versions.
The error output seems to be coming from command line git (since it is prefixed with "stderr:" and that string does not appear in the git plugin or the git client plugin).
You may also want to test drive a newer version of Jenkins and a newer version of the git plugin, in case they are better behaved in that area. I'm not aware of any changes that would be relevant, but those versions are at least 18 months old. A Docker instance is available which allows you to test drive new Jenkins versions more easily.
Mark Waite