Your screenshot reveals that the last analysis had 2 warnings: I suggest you investigate them. Particularly if they relate to SCM issues.
I also noticed in your screenshot you’re running our Data Center Edition, which means you or your company almost certaily have access to our commercial support team. I suggest you file a ticket with us via that channel.
Now that you’ve eliminated the warnings as a source of potential problem, the next steps I can suggest:
Confirm whether it’s really true the file(s) involved in those issues really weren’t changed as part of the PR. If you drill all the way into the issue where you can see the code in its context, what does the “blame” data in the left margin tell you about the commit SonarQube sees this was a part of? Is it really not a commit involved in the PR?
Check your analysis logs for anything strange involving the file(s), e.g. character encoding warnings or anything like that
FYI, We’ve made improvements in the configuration and calculation of what is “New Code” in the new 8.9 LTS release. I encourage you to consider an upgrade along with investigating internally to see about your access to our commercial support team.
We managed to make SonarQube correctly recognize New Issues.
After enabling full clone BOTH for the master branch and for the Pull Request branches, SonarQube started to recognize New Issues correctly (enabling full clone for only the master branch or for the PR branch didn’t make any difference).