Some maintainers generate their debian/changelog files from commit messages in Git using e.g. gbp dch. The janitor attempts to autodetect whether or not the changelog file should be updated along with any changes, by looking at the packages commit history and whether or not it has a [dch] section in debian/gbp.conf.
If this autodetection does not work correctly, then you can force it to not update the changelog by adding a [dch] section to your debian/gbp.conf or get it to (not) update the changelog by setting the update-changelog = False|True flag in debian/lintian-brush.conf.
Bug reports about broken autodetect would also be most welcome.