All three of of your loops use the same global variable ($_). Declare a lexical variable for at least two of them.

#UNTESTED
RESULT: foreach my $wrd(@result)
        {
            my %seen;
            $seen{$_}++ for (split //,lc $_);
            
            foreach my $ltr (keys %seen)
            {
                next RESULT if ($seen{$ltr} > $master_letter_freq{$ltr
+});
            }
        
            print "$_\n";
        }
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UPDATE: Thanks to jo37 (below),I now believe that the original code 'should' work.