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I'd guess then that the portion which exposes the misconfiguration in your Jenkins job or Jenkins environment to the git plugin is at line 255 and 256 where the comment says:
// add env contributing actions & values from last build to environment - fixes
JENKINS-22009That's the key change which was in that commit. As far as I can tell, it is doing "the right thing" by making the environment variables available inside the plugin.
I think that its discovery of your EnvInject related configuration issue is a happy side effect, not a bug which the git plugin can fix.