## your original code
@{$sets{$fasta_id}[$setscounter]{$sitekey}} = grep {
     $_ >= $lowerlimit and $_ <= $upperlimit
}  @{$matches{$fasta_id}{$sitekey}};

##</code><code>##

@{$sets{$fasta_id}[$setscounter]{$sitekey}} = ();
foreach ( sort @{$matches{$fasta_id}{$sitekey}} ) {
    last if $_ > $upperlimit;
    next if $_ < $lowerlimit;
    push @{$sets{$fasta_id}[$setscounter]{$sitekey}}, $_;
}