It could be leading or trailing spaces, add TRIM to the sql and try s/\s//g in place of chomp on the @ldap elements. Use Data::Dumper to inspect the values. For example

#!/usr/bin/perl
use strict;
use DBI;
use Data::Dumper;

my $dbh = get_dbh(); #as required

# get mysql records
my $sql = "SELECT TRIM(mid),type FROM table
           WHERE type != 'NA'";
my $sth = $dbh->prepare($sql); 
$sth->execute();

my %table = ();
while (my ($mid,$type) = $sth->fetchrow_array){
  $table{$mid} = $type;
}
#print Dumper \%table;

# check ldap records
my @ldap = (" 4\r\n","  5  ","  6  ",7,8,9,1,2,3);
#print Dumper \@ldap;

my @new_ldap = ();
for my $id (@ldap){
  #chomp $id;
  $id =~ s/\s//g;
  if (exists $table{$id}){
    print "[$id] removed\n";
  } else {
    push @new_ldap,$id;
  }
}
#print Dumper \@new_ldap;
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