Well, I'll give this problem a go even though it has been beaten to death already. It's a bit long, but it works all the same.

use strict;

my %files;
my @files;

@files =<DATA>;
@files = map { s/\n//; $_ } @files;
close(DATA);

foreach (@files) {
    $files{substr($_,0,(length()-4))}++;
}

foreach (keys %files) {
    print "$_ is not matched and has a count of $files{$_}\n" if $file
+s{$_} == 1;
}

__DATA__
001.did
001.mrg
002.did
002.mrg
003.did
004.did
005.did
005.mrg
[download]

The output of this is:

C:\configs>perl test.pl
003 is not matched and has a count of 1
004 is not matched and has a count of 1

Of course, this code is nothing more than a modified "seen" loop. Not too fancy. One thing I should point out is that if you use  foreach (<*.mrg>), it'll do the same thing as your glob (because it is the same thing as far as I know). It's just shorter. Hope that sparks a few ideas.