If a Git SCM checkout is configured with multiple repositories then all change sets for the build will use GitHubProjectProperty value for URL when building change links.
If I were to trigger a build by pushing a change to 'https://github.com/Organization/repo-two' then the change set links would be 'https://github.com/Organization/repo-one/commit/<CommitId>' resulting in a 404.
To clarify this still happens even if the repositories are broken into seperate SCM checkouts in a single pipeline. Issue is slightly mitigated by declaring the repository browser type on the individual checkouts.
This also occurs on non pipeline jobs as well.