I am not sure how the SonarQube identifies the changed lines in the current version vs the previous one. According to this reply, I understand it is based on a diff with the current state of develop.
So, I wonder if the issue we are facing for the develop branch is because there is a lot of activity in our repository, and many developers are merging almost at the time into the develop branch. So, often, when the SonarQube analysis is running for the next merge, a couple of other merges are done already.