Update:
I have now narrowed down the issue to using a specific gradle plugin. In our case, we are using a gradle plugin to manage Git hooks in all of our repositories and removing this plugin fixes the issue. This issue is particular to JGit as the blame command doesn’t work with this plugin (but the blame command works for JGIT versions less than or equal to 5.5.1 even when this plugin is used, smh). So when this gets fixed by JGit, sonar scans should work as normal.
@Colin It might be worth adding this information to sonarqube’s documentation if the team agrees and hope they start looking at alternatives to JGit in the future