Look in the XMl file for instances where you have multiple <Hit_hsps> tags within a <Hit> or multiple <Hsp> tags within a <Hit_hsps>.

This test data replicates your error

<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://ww
+w.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
<BlastOutput_iterations>
<Iteration>
<Iteration_hits>
<Hit>
  <Hit_num>1</Hit_num>
  <Hit_def>Uncultured Sulfuricurvum sp. RIFRC-1, complete genome</Hit_
+def>
  <Hit_hsps>
    <Hsp>
      <Hsp_identity>16</Hsp_identity>
    </Hsp>
  </Hit_hsps>
</Hit>
<Hit>
  <Hit_num>2</Hit_num>
  <Hit_def>Neosartorya fischeri NRRL 181 conserved hypothetical protei
+n (NFIA_106270) partial mRNA</Hit_def>
  <Hit_hsps>
    <Hsp>
      <Hsp_identity>16</Hsp_identity>
    </Hsp>
  </Hit_hsps>
  <Hit_hsps>
    <Hsp>
      <Hsp_identity>16a</Hsp_identity>
    </Hsp>
    <Hsp>
      <Hsp_identity>16b</Hsp_identity>
    </Hsp>
  </Hit_hsps>
</Hit>
</Iteration_hits>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>
[download]

#!perl
use strict;
use warnings;
use XML::Simple;
use Data::Dump 'pp';

# force these tags into array
my $blast = XMLin('BLAST2.XML',ForceArray=>['Hit','Hit_hsps','Hsp']);

my $hits = $blast->{BlastOutput_iterations}->{Iteration}->{Iteration_h
+its}->{Hit};
my $ret;
foreach my $hit (@{$hits}) {
  my @Hsp_identity;
  for my $Hit_hsps ( @{$hit->{Hit_hsps}} ){
    for ( @{$Hit_hsps->{'Hsp'}} ) {
      push @Hsp_identity, $_->{'Hsp_identity'}
    }
  };
  
  push @{$ret},join '|', 
    $hit->{Hit_def},
    $hit->{Hit_num},
    @Hsp_identity;
};
pp $ret;
[download]