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
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