A rewrite (yes, I've changed the coding style slightly...): (Be forewarned that this is very much untested.)

#!/usr/bin/perl -w
use strict;

my $home          = $ENV{HOME} || (getpwuid($<))[7];
my $mail_to       = 'me@employer'; # XXX when is this used?
my $outfile       = "$home/store_errors";
my $delivery_dir   = "$home/delivery";
my $no_curropt_dir = "$home/no_curropt_stores";

my $error_pat      = "$delivery_dir/error*";
my $no_error_pat   = "$delivery_dir/no_error*";
my $corrupt_pat    = "$no_curropt_dir/corrupt*";
my $no_corrupt_pat = "$no_curropt_dir/no_corrupt*";

my $store_list = "/store_list.full_listing";

my $date = scalar localtime;

exit unless `netstat -i` =~ /^P01$/mi;

sub store_name_map {
  map { (split /\./, $_, 2)[1] } @_
}

sub uniques {
  my %seen;
  $seen{$_}++ for @_;
  return sort grep { $seen{$_} == 1 } keys %seen;
}


open STORES, "<$store_list" or die "opening $store_list for reading: $
+!\n";
my @stores = <STORES>;
close STORES;


my @errors    = store_name_map(glob($error_pat));
my @no_errors = store_name_map(glob($no_error_pat));
my @error_union= uniques(@stores,@errors,@no_errors)
my @corrupt   = store_name_map(glob($curropt_pat));
my @no_curropt= store_name_map(glob($no_curropt_pat));
my @curropt_union= unqiues(@stores,@corrupt,@no_curropt);



my $store_count = scalar(@stores);

my $error_count  = @errors + @no_errors; # - $store_count;
my $curropt_count = @curropt + @no_curropt; # - $store_count; 
# XXX what were the - $NUM_STORES for?

my $no_error_count = $store_count - $error_count;
my $no_curropt_count = $store_count - $curropt_count;

open OUTFILE, ">$outfile" or die "opening $outfile (for writing): $!\n
+";
local $" = "\n\t\t"; # proper array output format
print OUTFILE <<"END";
<snip> listing for $date
Error Section
There were a total of $store_count stores.
\tThere were $error_count stores that reported in.
\tThere were $no_error_count that did not report in.
\t\t@error_union
\tThere were $error_count that reported errors.
\t\t@errors

Curroption Section
There were a total of $store_count stores.
\tThere were $curropt_count stores that reported in.
\tThere were $no_curropt_count stores that did not report in.
\t\t@corrupt_union
\tThere were $curropt_count that reported errors.
\t\t@corrupt
END
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I guessed in a few places what you wanted to do.

This is probably a lot more wasteful then yours would be if it worked, due to not using temperorary files; that could probably be remidied with a bit of work. I hope that this helps you learn how to code better...