SonarQube Enterprise 2026.03 PR Analysis Reporting Issues on Unmodified Files; Issues Disappear After Rebase
Hello Community,
We are using SonarQube Server Enterprise 2026.03 and have observed inconsistent behavior during Pull Request analysis.
Issue Description
PR analysis occasionally reports issues on files that are not modified as part of the Pull Request. The reported issues may include Bugs, Code Smells, Vulnerabilities, or Security Hotspots.
Observations
- The impacted files are not included in the PR changes.
- Git diff confirms that these files were not modified in the feature branch.
- The issues appear only during PR analysis.
- After rebasing the feature branch with the latest target branch and re-running the analysis, the reported issues disappear.
- This behavior has been observed across multiple repositories and PRs.
- No corresponding code changes exist that would explain the newly reported issues.
Environment
- SonarQube Server: Enterprise 2026.03
- Deployment Type: Zip
- SCM: Git / Bitbucket
- CI/CD: Jenkins
- Scanner Version: sonar-scanner version 12 docker image- SonarScanner CLI 8.0.1.6346 and mvn sonar plugin:5.5.0.6356
- New Code Period 7 Days
Expected Behavior
PR analysis should report issues relevant to the current PR changes and should not introduce issues for files that are not part of the Pull Request.
Actual Behavior
Issues are reported on unchanged files during PR analysis. Rebasing the branch against the latest target branch and re-running the analysis resolves the issue.
Questions
- Is this expected behavior in PR analysis?
- Could an outdated branch reference, merge base calculation, or issue synchronization problem cause this behavior?
- Why does rebasing the branch resolve the issue?
- Are there known issues in SonarQube Enterprise 2026.03 related to PR analysis on stale branches?
- What is the recommended approach to prevent such issue inconsistencies in future PR analyses?
guidance would be appreciated.
Thank you.