Perhaps I'm missing something, but here's what I got:

my @a = ( 1,1,1,1,1,2,2,2,3,3,4,5,6);
my @b = ( 1,2,3,4,5,6 );

my @c = map {
    my $found = 0;
    my $m = $_;

    for (1 .. @b)
    {
        my $n = shift @b;
        ++$found and last if $m == $n;
        push @b, $n;
    }

    $found ? () : $m;
} @a;
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Update: OK, I think I got it to work. No hash here, so it may save more space at the expense of time.