The other case where I have seen that error message in non-git upload-pack context (as opposed to my previous answer) is in this thread:
GitHub has a bug where, if someone submits a pull request to a project, and then that entry is deleted (I don't know if it's that they just delete a pull request, or they delete their fork/account, but something), then you get these stale references.
Somewhere on GitHub, there's a support thread for this.
If that upstream repo you are cloning isn't a Github repo, and if you have access to said upstream repo, then a git fsck
or git fsck --lost-found
could help.
Since it is a GitHub repo, the OP rderoldan1 took the right action and wrote to GitHub support, and reports in the comments:
they respond me:
"We've found the cause of the problem, and are just working to resolve it.
It appears that the Git repository on the file server has been corrupted and requires a bit of manual wire uncrossing. Rest assured, our systems team is looking into it, and hope to have an update for you soon."
rderoldan1 reports the result from GitHub:
Today 9 oct, Jeff King send me and email, and now mi git is working :D, here is his message, thanks to @VonC and GitHub staff
The problem with your repository is fixed.
One of the objects from a pull-request's test-merge was missing on our end, causing git to complain. This is due to a bug on our end that we're still tracking down.
In the meantime, I've restored the missing object, and the repository should be in good shape now.