Could the problem be that I have more than one value in some of the keys?

Yes. 

foreach my $intersect_file(@intersect_keys) {
    my $exec = $system_file_data{$intersect_file};
    my @values = ref $exec ? @$exec : ($exec);
    print "$_\n" for @values;
}

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See perlreftut and perldsc for more information about nested structures.

In reply to Re^5: Need to get the intersect of hashes by moritz
in thread Need to get the intersect of hashes by jbush82

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