For instance:
It returns:
User - Email
Smith, Joe - Joe.Smith@perlmonks.com
Smith, Joe(2) - Joe.Smith@perlmonks.com
instead of:
User - Email
Smith, Joe - Joe.Smith@perlmonks.com
Smith, Joe(2) - Joe.Smith2@perlmonks.com
[download]

#!perl

use Getopt::Long;
use Net::LDAPS;
use Text::CSV;

($domainCont, $surNm, $givenNm, $dispNm, $eNo, $outFlNm, $id, $pw) = (
+'', '', '','', -1, '', '', '');

&GetOptions('dc=s'  => \$domainCont
           ,'i=s'   => \$id
           ,'p=s'   => \$pw
           ,'d=s'   => \$baseDir
           ,'f=s'   => \$inFlNm);

my $ad = Net::LDAP->new($domainCont) or die "Can't connect to AD >$!<\
+n";
$ad->bind($id, password=>$pw) or die " bind for $id failed >$!<\n";

my $base = 'OU=People,OU=staff,DC=ad,DC=wjgilmore,DC=com';
my $attrs = "sn, givenname";

open IN, "<"."./$baseDir/$inFlNm" or die "Can't open transfers file >$
+inFlNm<\n";
$outFlNm = "test.csv";
open OUT, ">"."./$baseDir/$outFlNm" or die "Can't open transfers file 
+>$outFlNm<\n";
print OUT "Name,,,Assistant\n";

while(<IN>){
    @mngr = split(/"/, $_);
    @manager = split(/, /, $mngr[1]);
    $mFName = "$manager[1]"; 
    $mLName = "$manager[0]"; 
    @assist = split(/,/, $mngr[2]);
    @assistant = split(/ /, $assist[1]);
    chomp($assistant[1]);
    $aFName = "$assistant[0]";
    $aLName = "$assistant[1]";
    $lenMFName = length($manager[1])*.5;
    $lenAFName = length($assistant[0])*.5;
    substr($manager[1],-$lenMFName)=$pmFName;
    substr($assistant[0],-$lenAFName)=$paFName;

    $filter1 = '(&(sn='.$mLName.')(givenname='."$manager[1]*".'))';
    $filter2 = '(&(sn='.$aLName.')(givenname='."$assistant[0]*".'))';
    my $results1 = $ad->search(base=>$base,filter=>$filter1,attrs=>$at
+trs);
    my $results2 = $ad->search(base=>$base,filter=>$filter2,attrs=>$at
+trs);
    $x1 = $results1->count();
    $x2 = $results2->count();
    
    if($x1 > 0){
        foreach $adEnt ($results1->entries){
            my $entry1 = $results1->entry($i1);
            my $mail1 = $entry1->get_value('mail');
            foreach $adEnt ($results2->entries){
                print OUT "$mFName,$mLName,";
                print OUT "$mail1,";
                my $entry2 = $results2->entry($i2);
                my $mail2 = $entry2->get_value('mail');
                print OUT "$aFName,$aLName,";
                print OUT "$mail2,\n";
            }
        }
    }
    else { 
        if($x2 > 0) {
            print OUT "$mFName,$mLName,Not Found,";
            foreach $adEnt ($results2->entries){
                my $entry2 = $results2->entry($i2);
                my $mail2 = $entry2->get_value('mail');
                print OUT "$aFName,$aLName,";
                print OUT "$mail2,\n";
            }
        }
        else {
            print OUT "$mFName,$mLName,Not Found,$aFName,$aLName,Not F
+ound";
        }
    }
}
$ad->unbind;
[download]

First I'd add use strict; use warning;. At the very least, $i2 is not defined.

Second, I'd add a "\n" at the end of print OUT "$mail1,";

Third, I don't see how the code you posted writes what you say it did. (I don't, for example, see hyphens in any of your prints.)

Ok I added strict and warning and I just removed $i1 and $i2 from where they were. I do not need a \n due to how I want the output displayed. There are hyphens all over the place, if you don't see a hyphen at the end of the line see the next line and if there is a + in the front of the line it means that it is a continuation of the previous line.