I don't get any warnings. What I do notice is that space is included in the [...] parts. So here's a small fix:

sub consensus {
  ... # code from before, until:

    # store only those who occur the most times
    my @most = grep $freq{$_} == $max, keys %freq;              
    @most = grep $_ ne " ", @most if @most > 1;
    push @cons, \@most;
  }

  return \@cons;
}
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And to get the string version, I use:

sub consensus_to_string {
  my $con = shift;
  my $str;

  for (@$con) {
    if (@$_ > 1) { $str .= "[" . join("", @$_) . "]" }
    else { $str .= $_->[0] }
  }

  return $str;
}
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