Silent Merge Queue Bug Corrupted 658 GitHub Repositories
Original: The Silent Merge Queue Corruption That Hit 658 GitHub Repos
Why This Matters
Demonstrates how feature flag failures can silently corrupt version control systems
GitHub's merge queue feature silently corrupted 658 repositories on April 23, 2026 due to an incomplete feature flag gate. The bug affected multi-PR squash merge groups for 3.5 hours, creating valid-looking commits that reverted prior work while monitoring systems showed no issues.
GitHub deployed a change to its Pull Requests service that introduced a new merge-base computation path for merge queue ref updates. An incomplete feature flag allowed the unreleased code to run in multi-PR squash merge groups, causing the system to choose wrong bases for three-way merges. This created commits that appeared to advance the default branch while silently dropping previously merged changes. The issue affected 658 repositories and 2,092 pull requests over 4 hours 38 minutes. GitHub's monitoring systems detected no problems because requests, latencies, and errors remained normal - the service was operating but producing incorrect results. Users first noticed merged pull requests missing expected changes from HEAD. GitHub became aware at 19:38 UTC after support inquiries increased, traced the issue to the faulty feature flag, and deployed a fix by 20:43 UTC. No commits were lost, but affected repositories required manual remediation instructions sent to administrators.