If the main list is always going to be in a section, try triggering twig_roots on '/section/list' instead of just list.

Otherwise add a test so you don't print the nested list: print unless( $sec->in( 'list')), or return if the list is nested:

#!/usr/bin/perl
use strict;
use XML::Twig;
my $twig = XML::Twig->new( twig_handlers => { list => \&list}, pretty_
+print=> 'indented');

$twig->parse( \*DATA);

sub list 
  { my ($twig, $list) = @_;          # I renamed $sec as $list
    return if( $list->in( 'list'));
    $list->print; 
  }

__DATA__
<?xml version="1.0"?>
<camelids>
  <section>
    <r>afasdfasdf</r>
    <section>
      <list>
        <list-item>242354</list-item>
        <list-item>gsdfg
          <list>
            <list-item>7989</list-item>
            <list-item>97989</list-item>
          </list>
        </list-item>
      </list> 
      fasdfas
    </section>
  </section>
</camelids>
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