If a submodule is in the location that an artifact used to be at, the plugin will cause a failure.
GitSCM.java should be updated to move
I would submit a patch for this except for JENKINS-8314
Clean After Checkout Results in Failed to Checkout Revision
Integrated in plugins_hudson-git-plugin #53
JENKINS-8315 Moved git clean to happen before submodule update
Andrew Bayer :