i added a line marked with # fix as i explained, there is a bug in the code you used to rearrange: you must add the fix pos($s)=pos($s)+1-length $1; at the end of the while:;

sub oha {
    my $s=shift;
    my %saw;

    while($s =~ /(..+)(?=.*?\1)/g) {
        for my $x (0..length $1) {
            @saw{ map {substr $1, $x, $_} $x+2..length $1 } = ();
        }
        pos($s)=pos($s)+1-length $1; # fix
    }
    $saw{$_} =()= $s =~ /\Q$_/g for keys %saw;
    \%saw;
}
[download]

i apologize for the bug

Oha