The default value of git config core.commentChar is #. It appears that Sourcetree expects this to be the comment character and does not behave well if the value is changed to something else.

When selecting "Rebase children of hash interactively...", there are several rows of "commits" that are not actually commits—they are comments that Git has added to the file it produces when you run git rebase --interactive hash.

Please respect the value of git config core.commentChar when parsing the output of git rebase --interactive.

The solution right now is to temporarily remove my customization of the core.commentChar value and revert it back afterward.