I expect that really the only test you want to perform on the list of SOAs for a single domain is whether or not they are all the same. If there are any differences then that should be treated as a problem.

So, instead of your test being if ($serials[0] == $serials[1]) try instead finding how many unique values are in the list, eg.

use List::MoreUtils qw/uniq/;

if (scalar (uniq @serials) == 1) {
  say $resultsfh join (',', 'MATCH', $fqdn, @serials);
} else {
  say $resultsfh join (',', 'MISMATCH', $fqdn, @serials);
  push @errors, join (',', 'MISMATCH', $fqdn, @serials);
}
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