PR excludes wrong issue

I ran into this issue as an extension of 'New Code' shows issues introduced on Reference Branch.

  1. Create a new project by doing a scan of an existing git repo on the master branch
  2. This isn’t required, but should put the system in a known state
  3. Set the “New Code” to reference the master branch
  4. This may or may not be relevant
  5. Scan master branch
  6. Make a new branch locally from the same commit as master
  7. Scan the new branch
  8. Make a new commit that adds issues on the new branch
  9. Scan the new branch
  10. This shows 6 new issues
  11. Switch back to the master branch
  12. Make a commit with an issue in a different file on the master branch
  13. Scan the master branch
  14. Merge the master branch into the new branch
  15. Scan the new branch
  16. Shows 10 issues (6 from new branch, 4 from master)
  17. Flag one new issues from the new branch as ‘won’t fix’
  18. Make a PR from the new branch to inc2

Preferred behavior: Shows the 5 issues that were left uncommented from the new branch
Expected behavior: (based on Dealing with False positives,wont fixes): Shows all 6 issues introduced in the new branch (including the one marked as ‘won’t fix’ in the branch)
Actual behavior: Shows 5 issues from the new branch, but the one that is missing is not the one marked as won’t fix.