Yes,
changing a couple of lines on a single files results in raising violations in the whole file.
All of those violations are listed in the summary comment on PR.
The really modified lines are additionally annotated with inline comments, but AFAIK GH API rejects annotation to lines that were not modified in a PR.
Can I somehow turn on some debug on a sonar analyser to check why this is happening?
My repose are private so I cannot share an example.