This creates the full graph before filtering to your length requirements

use strict;
use warnings;
use Data::Dump qw/pp dd/;

my @words = data();
my (%lower,%super);

for my $word ( sort {length $a <=> length $b} @words ) {
    
 SUPER:
    for my $sub ( keys %lower ) {
        if ( -1 != index ($word,$sub) ) {
            for ( @{$super{$sub}} ) {
                next SUPER if  -1 < index ($word,$_)
            }
            push @{$super{$sub}},$word;
        }
    }

    $lower{$word}=1;

}



#pp \%super;


for my $key ( keys %super ) {
    if (length $key >8) {
        delete $super{$key};
        next;
    }

    $super{$key} = [grep { length $_ > 8 } @{$super{$key}}];
    
}

pp \%super;

sub data {
    return
    "funk", "fungibles", "funneling", "fundraiser",
    "fungi", "functions", "fun", "fundamental", "functioned",
    "functional", "functioning", "funicular", "funnel",
    "functionaries", "functionary", "funkiness", "function",
    "fungicidal", "fungible", "fungicide", "fundraising", "funniness",
    "fund", "funereal", "funereally","fundraising-team",
}
[download]

{
  fun => ["funicular", "funniness"],
  function => [
    "functions",
    "functioned",
    "functional",
    "functioning",
    "functionary",
    "functionaries",
  ],
  fund => ["fundraiser", "fundamental", "fundraising"],
  funereal => ["funereally"],
  fungi => ["fungicide", "fungicidal"],
  fungible => ["fungibles"],
  funk => ["funkiness"],
  funnel => ["funneling"],
}
[download]

Disclaimer: data mostly stole from tybalt89 :)