You didn't show us what you expect to be printed. But, when I fix the compile errors in the code you posted, then run it, I get the following output:

./foo.log
Use of uninitialized value $uid in join or string 
|61110530R_000001.jpg|8|fb0ff0b498cb6ce79df20fdddd71da3f|08141ce3c84cb
+54d57d40b5023312c53
Use of uninitialized value $uid in join or string 
|61110530R_000002.jpg|8|7b44c390f7279a3f266652a96a5f686d|462db8d6b278f
+6fdb63f87fd2974e7e9
Use of uninitialized value $uid in join or string 
|61110530R_000003.jpg|8|8acd6e39a21f0fc18dfb6a54663fa472|7e9c7959e3a3b
+60c4d2f80e089f03f9d
Use of uninitialized value $uid in join or string 
|61110530R_000004.jpg|8|f655a572365bcea7c878201b7606d68a|0fbdfb7ba703e
+0ad810025135e4e8070
Use of uninitialized value $uid in join or string 
|61110530R_000005.jpg|8|2a055f3579db7f9c583c8cf84afdf030|50a8ee3e882b7
+9de5fe8a47be54cc478
Use of uninitialized value $uid in join or string 
|61110530R_000006.jpg|8|8dfa19092cdf0d76bf99eede88faee19|3380c9f79217b
+a0faee294ab9cffdb81
Use of uninitialized value $uid in join or string 
|61110530R_000007.jpg|8|97d8a953cc1b8ab1dff728a8b08146be|37fa1505f9ca1
+3251406658653af4439
Use of uninitialized value $uid in join or string 
|61110530R_000008.jpg|8|638a7f3cb7d2b189751c62c91e018d28|d008d5852cfaf
+f6cf14fa0748b5d044f
[download]

Update: At AM's request, here is a compilable version of the OP's code (2 extra curlies at the end):

#!/usr/local/bin/perl

use strict;
use warnings;
use Data::Dumper;

$/ = "";

my @InputFiles = (</usr/mlm/qa/logs/hhl/BATCH*/*/*_checksum.log>);


foreach my $InputFile ( @InputFiles ) {

  print "$InputFile\n";

    my %errors;

    open my $input_fh, '<', $InputFile
      or die "Can't open input file ($InputFile): $!";

    my $uid = <$input_fh>;
    ($uid) = $uid =~ /UID=(\S+)/;

    while ( my $record = <$input_fh> ) {
        my ($md5)      = $record =~ /METS:.+?MD5=(\S+)/;
        my ($filename) = $record =~ /Filename=(\S+)/;
        #my ($error)    = $record =~ /[Error] +MD5=(\S+)/;
        my ($error)    = $record =~ /\Q[Error]\E .+MD5=(\S+)/;

        if ( $error ) {
            $errors{$filename}{md5}      = $md5;
            $errors{$filename}{computed} = $error;
        }
    }
    close $input_fh;

    my $count = keys %errors;


     foreach my $filename ( sort keys %errors ) {
        print join('|', $uid,
                      $filename,
                      $count,
                      $errors{$filename}{md5},
                      $errors{$filename}{computed}
                ),"\n";
     
     }
}
[download]