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Just ran into this error. I will attempt restarting the server, but otherwise it's locked up.
Edit:
Alright I restarted my server and it didn't make a difference. I noticed that git was checking out origin/master but when it was building it was referencing origin1/master. I believe this was caused because I added a second git repo and removed it.
The work around was to copy the job to a new one.
Edit 2:
I've been able to recreate this issue by creating a project that checks out from some repo, then in a bash script during the build process, performing a git clone on some other repo (it's crazy, yeah..).