First off, a couple of style issues:

• If you find yourself writing the same code over and again put it in a sub
• Don't use map in place of for used as a statement modifier

With that somewhat in mind consider the following:

use strict;
use warnings;
use List::Util;

my %candidate = CountWords ('the the the the the the the');
my %reference = CountWords ('the cat is the on the mat');
my %counts =
    map {$_ => List::Util::min ($candidate{$_} || 0, $reference{$_} ||
+ 0)}
    keys %candidate, keys %reference;

print "$_: $counts{$_}\n" for sort keys %counts;


sub CountWords {
    my ($sentence) = @_;
    my @words = split (/\W/, $sentence);
    my %wordCount;

    ++$wordCount{$_} for @words;
    return %wordCount;
}
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Prints:

cat: 0
is: 0
mat: 0
on: 0
the: 3
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