You have a big glaring bug here:

          if (@arrayA && $hit == length(@{$matches{$fastarray[$h]}{$si
+tekey}})) {
            $sets{$fastarray[$h]}[$setscounter]{$sitekey} = \@arrayA;
            print "\$sets{$fastarray[$h]}[$setscounter] is:\n";
            print Dumper(%{$sets{$fastarray[$h]}[$setscounter]}); 
            @arrayA = ();
            }
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You are assigning a reference to @arrayA and then clearing out the contents of @arrayA so it is the same as assigning an empty anonymous array in the first place. Remove the line: "@arrayA = ();". Anyway, it looks like your code could be simplified to:

for my $fastarray ( @fastarray ) {
    my $hash = $matches{ $fastarray };

    for my $site ( sort { $a <=> $b } keys %$hash ) {

        for my $lowerlimit ( @{ $hash->{ $site } } ) {
            my $upperlimit = $span + $lowerlimit;

            for my $sitekey ( sort { $a <=> $b } keys %$hash ) {
                push @{ $sets{ $fastarray } }, { $sitekey => undef };
                my @arrayA = grep { $_ >= $lowerlimit && $_ <= $upperl
+imit } @{ $hash->{ $sitekey } }
                    or next;
                $sets{ $fastarray }[ -1 ]{ $sitekey } = \@arrayA;
                print "\$sets{$fastarray}[-1] is:\n", Dumper $sets{ $f
+astarray }[ -1 ];
                }
            }
        }
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