Based on my last code, you could add a hash with the number of occurrence of every pair and then check if this pair was already matched this often:

use strict;
use warnings;

my $word = "zezlze";
my $dictword = "zezezd";

my @pairs = $word =~ /(?=(..))/g;
my %count;

$count{$_}++ foreach (@pairs);

my $matcher = qr/(?=(@{[join "|", @pairs]}))/;


my %seen;
my $matches = 0;
my @matches;
foreach my $match ($dictword =~ /$matcher/g) {
    if ($seen{$match}++ < $count{$match}) {
        $matches ++;
        push @matches, $match;
    }
}

print "Matches: @matches\n";
print "$matches $dictword \n";
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results in

Matches: ze ez ze
3 zezezd
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