Unable to update repository refs: fatal error in commit_refs and HTTP 500

[liangruiyuan-max]

🏷️ Discussion Type

Bug

Body

My private repository TwoAppGuard cannot update its Git references. An ordinary fast-forward push from 5a46528 to 3027d5b fails with remote: fatal error in commit_refs. GitHub’s compare API reports that the new commit is one ahead and zero behind, and the new commit is readable by SHA.

I have ADMIN and push permissions; the repository is not locked, archived or disabled, and its settings show no rulesets or classic branch protection. Non-force REST and GraphQL reference updates returned server errors. The REST request at 2026-11-05 00:23:27 UTC returned HTTP 500 with request ID B020:57BCC:55967C:118EE7C:6AEBCC7C. Creating a tag and creating a branch from the target commit in the GitHub web UI did not succeed.

I also tested pushing 3027d5b to a previously nonexistent recover-main branch. It was rejected with the same commit_refs error. A new empty successor commit with the same file tree was rejected when pushed to that branch as well. No force push has been used.

GitHub Support ticket 4953172 was closed without investigation because my account is eligible for self-service resources. Could a GitHub staff member help investigate the reference update failure or advise how to have the repository inspected? I can provide the private repository URL through an appropriate private channel if needed.

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[imsai-sh]

Independent reproduction on a different account and repository, same day. Repository id 1445879739.

Symptoms, identical to the original post:

• git push → remote: fatal error in commit_refs, ! [remote rejected] HEAD -> <name> (failure). Reproduced over SSH and HTTPS, with and without --no-thin, and with branch names both containing and not containing a /.
• POST /git/refs → 422 Reference update failed, for refs/heads/* and refs/tags/* alike, including when the target SHA is a commit already present in the repository — so the request carries no new objects at all.
• PATCH /git/refs/heads/main set to the SHA it already points at, a complete no-op → HTTP 500, empty body, X-GitHub-Request-Id: B5A0:123F9F:4C0A60:7CDE90:6AEBD166, Date: Thu, 05 Nov 2026 00:44:24 GMT. That is about 21 minutes after the request ID in the original post.

What still works, which narrows it to the ref layer:

• All reads are fine: clone, ls-remote, REST and GraphQL.
• POST /git/blobs → 201. The object store is writable.
• The commit the push was trying to publish, a148e6d0f968eff9eaec8d275f9f1f4e3f24857a, is already readable via GET /git/commits/.... The push transferred its objects successfully and failed only at the ref update.

Control, same account, same SSH key, same token, same local objects: a repository created minutes earlier accepts POST /git/refs for both a branch and a tag, accepts the identical git push first try, and returns 200 on the same no-op PATCH. So this is isolated to the affected repository, not to the account or the client.

The repository was unremarkable: created through the web UI, public from creation, exactly one ref (refs/heads/main), zero tags, two commits, two ordinary pushes — one to an empty repository, one fast-forward. No force-push, no --mirror, no wholesale refs/* push, no history rewrite, no ref deletions, no rename, no visibility change, never imported or migrated. No rulesets, no branch protection, not archived, not disabled, account has admin.

Support ticket #4953269 was auto-closed with the same self-service reply and without the repository being inspected, the same as #4953172 above.

That makes at least three repositories across three accounts on 2026-11-05: this one, TwoAppGuard, and repository 1440183363 from the other thread. Request IDs are available for staff to trace.

[iqonli]

Another affected repository iqonli/MusicCardX

I am experiencing the same Git reference update failure on my public repository:

https://github.com/iqonli/MusicCardX

As of November 5, 2026, I am unable to create any new Git tags or publish GitHub Releases.

Reproduction results:

• Git push: remote: fatal error in commit_refs
• REST API POST /git/refs: HTTP 422, Reference update failed
• GitHub CLI Release creation: HTTP 500
• GitHub web Release creation: HTTP 500
• Read-only Git operations and API requests work correctly.
• Creating a completely different tag fails identically.

I have verified that:

• I am the repository owner with admin and push permissions.
• My OAuth token has the repo scope.
• The repository is neither archived nor disabled.
• Immutable Releases are disabled.
• No repository rulesets are configured.
• The target commit exists and is readable.

GitHub Support ticket #4953421 was closed with a self-service response without a technical investigation.

I have now found multiple independent repositories reporting the same commit_refs failure on November 5, 2026.

This suggests a possible GitHub-side reference transaction issue affecting multiple repositories.

Could a GitHub engineer investigate whether these failures share a common cause and advise how affected repositories can be restored?

Thank you.

[iqonli]

My issue has been resolved. Take a look at https://github.com/iqonli/MusicCardX/releases/tag/v1.5.0

[albertogunz]

Another independent reproduction on a separate account: albertogunz/in-a-nutshell (private repository).

Symptoms, matching this thread and @imsai-sh's report:

• git push fails with remote: fatal error in commit_refs and ! [remote rejected] ... (failure).
• REST POST /git/refs returns HTTP 422.
• Ref updates fail on existing branches and on previously nonexistent branch names.
• The commit objects themselves reach GitHub; the failure occurs only at the reference-update step.

No force-push, history rewrite, ref deletion, or repository recreation has been attempted.

Support: ticket #4953630 was closed with the self-service entitlement response, without technical investigation. That is the same outcome as #4953172 (this thread), #4953269, #4953421, and #4953811 (#212116).

Pattern: at least six repositories across separate accounts are now reported with the same commit_refs failure since Nov 4-5, 2026 (this thread, #212102, #212116, and the replies here). Two reporters (iqonli/MusicCardX and a reply in #212116) say the problem later cleared without any client-side change, which points to GitHub-side state rather than local configuration. Timing follows the Nov 4 Git Operations incident (https://www.githubstatus.com/incidents/smtdswd1h2w4).

Request to GitHub staff: could someone check whether these failures share a common cause in the reference-transaction layer, and whether affected repositories need server-side repair or are expected to recover on their own? Additional diagnostics can be provided through a private channel. Thank you.

[helioholthausen-HHH]

Another affected repository/account: helioholthausen-HHH/ConnectionDesignHub (GitHub.com).

Two authenticated attempts to create a branch on 2026-11-05 failed with the same remote error:

remote: fatal error in commit_refs

Client-observed response times (America/Sao_Paulo; not GitHub server timestamps):

• 20:22:23.982
• 20:23:24.826

Post-failure readback found that the expected remote branch was absent, with no corresponding draft PR or Actions run. The local branch and commit were checked; no force-push or history rewrite was attempted. We captured no GitHub request ID.

GitHub Support ticket #4959570 was closed with the self-service support eligibility response, without a technical investigation.

Could GitHub staff check whether the affected repositories share a ref-update failure and advise when a normal push of the existing local commit can be retried safely? We are preserving the unpublished local commit, have not attempted alternate refs or force updates, and can provide further sanitized diagnostics if useful.