The array @global_els contains all elements, not just the elements associated with each $row_el. Although there are other ways to better achieve what you want, you could fix your code by adding one line:

foreach $row_el (@row_els) {
    print  "\t",$row_el;
    foreach $global_el (@global_els) {
        # add this line...
        next unless exists $score_of{$row_el}{$global_el};
        print  "\t",$global_el;
        print  ",",$score_of{$row_el}{$global_el};
    }
    print  "\n";
}
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BTW if you used warnings you would have got a host of "unitialised value" errors. Data::Dumper is a great help too in these situations.