I that case maybe you should be using the Name field as the key to your hash like this

$sql = "select * from scanner.vulnerabilities";
$sth = $dbh->prepare($sql);
$sth->execute or die "SQL Error: $DBI::errstr\n";    
my %ref;
while (my $row = $sth ->fetchrow_hashref() ){
    $ref{ $row ->{'Name'} }{'port'} = [ $row ->{'port'} ];
}
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Also, this code only needs to run once so you can move it up outside the while loop.