For the MediaWiki 1.23.4 release, a patch file was provided that was based on all files in Git, instead of just the files we provide in a tarball. As a result, the audience the patch is intended for (using tarball instead of Git), could not apply it cleanly without warnings.
The problem is that you installed 1.23.3 from a tarball, but the patch is based on an installation from Git. Files for testing purposes aren't included in the tarball, but the patch tried to change one of them, which is why it couldn't find it. Your upgrade was successful even though you skipped that file.