Assuming there are any number of  space \t \r \n etc. at the end of each line, try something like:

c:\@Work\Perl\monks>perl -wMstrict -MData::Dump -le
"my $string = 'Return code is';
 ;;
 my %errors;
 for my $row (
   qq{2015/04/06 12:38:15 (9):(5564) Return code is :55\n\r\n},
   qq{2015/04/06 12:38:15 (9):(6600) Return code is :55 \r\n\r},
   qq{2015/04/06 12:41:31 (9):(3604) Return code is :1\t\n\r},
   ) {
   ++$errors{$1} if $row =~ m{ \Q$string\E \s* : (\d+) \s* \z }xms;
   }
 dd \%errors;
 ;;
 my $total;
 for my $err_no (sort { $a <=> $b } keys %errors) {
   print qq{error $err_no - $errors{$err_no} total};
   $total += $errors{$err_no};
   }
 print qq{total errors: $total};
"
{ 1 => 1, 55 => 2 }

error 1 - 1 total
error 55 - 2 total
total errors: 3
[download]

Something else isn't right then. Using the data you supplied above (which you should copy to your actual question for future readers), and copy/pasting Athanasius' regex, here's what I get in %errors:

use warnings;
use strict;

my $string = "Return code is";

my %errors;

while (<DATA>){
    ++$errors{$1} if /\Q$string\E \s* : \s* (\d+) $ /x;
}

while (my ($k, $v) = each %errors){
   print "$k: $v\n";
}
__DATA__
2015/04/06 12:38:15 (9):(5564) Return code is :55
2015/04/06 12:38:15 (9):(6600) Return code is :55
2015/04/06 12:41:31 (9):(3604) Return code is :1
[download]

Output:

1: 1
55: 2
[download]

I think it's the format of the input file. (UNIX)
I removed the $ from the regex and it works fine.
I don't quite understand why though.