Bingo! I thought so :) It is not a hash - it is hash of arrays and that's the place where you have to get familiar with references. $system_file_data{$intersect_file} gives you in return reference to an array, so you must do:

$array_ref = $system_file_data{$intersect_file};
@array = @$array_ref;
print @array;
# or
print $array[0];
[download]

Check the other hash, it should be accessible in similar way, too.