Typically, this message is the result of doing a shallow (partial) clone where, as you’ve noted, all branches are not available. At the very least, the target branch needs to be available so that a diff can accurately be done (and the PR will show the changed lines).
Make sure the target branch is fetched, or a full clone is performed, and you should be good to go. I also anticipate that accurately detecting changed lines will fix your other issue: