I can kinda duplicate your error with the following 

use strict; use warnings; 
use Data::Dumper; 
my $indexfile = {
                         'GCTCAGGA' => '4',
                         'AGCGTAGC' => '5',
                         'TTCTGCCT' => '3',
                         'CATGCCTA' => '6',
                         'TCGCCTTA' => '1',
                         'GTAGAGAG' => '7',
                         'GCGTAAGA' => '13',
                         'TAGATCGC' => '9',
                         'CTAGTACG' => '2',
                         'CTAAGCCT' => '16',
                         'CTCTCTAT' => '10',
                         'ACTGCATA' => '14',
                         'AGAGTAGA' => '12',
                         'TATCCTCT' => '11',
                         'AAGGAGTA' => '15',
                         'CCTCTCTG' => '8'
                       }; 
my $queryseq='';
for my $key (keys %$indexfile) {$queryseq.=$key;} 

print "First\n"; 
match_query($indexfile,$queryseq); 

print "second\n"; 
$indexfile->{a}=1; 
match_query($indexfile,$queryseq); 


sub match_query{
    my $indexfile = shift;
    my $queryseq     = shift;

print Dumper($indexfile); 
    
    my @match_count;
    for my $key (keys %$indexfile){
        my $count;
        for(my $k=0; $k<length($key)-1; $k++){
            my $k_nuc = substr $key,$k,2;
            for(my $i=0; $i<length($queryseq)-1; $i++){
                my $i_nuc = substr $queryseq,$i,2;
                
                my $rel = $k-$i;
                if($k_nuc eq $i_nuc){
                    $count->{$rel} ||= 0;
                    $count->{$rel}  += 1;
                }else{
                    $count->{$rel} ||= 0;
                    $count->{$rel}  += 0;
                }
            }
        }
        
        my @array = sort{$b <=> $a} values %$count;
        my $max_count = shift @array;
        my $element;
        $element->{bar} = $key;
        $element->{max} = $max_count;
        push @match_count, $element;
    
    }
    my $result;
    @match_count = sort{$b ->{max} <=> $a->{max}} @match_count; #CODE 
+#FAILS HERE DOESNT LIKE ->{max}
    if($match_count[0]->{max} == $match_count[1]->{max}){
        $result = 0;
    }elsif($match_count[0]->{max}>5){
      my $called_bar = $match_count[0]->{bar};
        $result = $indexfile->{$called_bar};
    }else{
       $result = 0;
    }
    return $result
    
}

[download]
Result 
First
$VAR1 = {
          'CTAGTACG' => '2',
          'ACTGCATA' => '14',
          'CTAAGCCT' => '16',
          'CCTCTCTG' => '8',
          'AGCGTAGC' => '5',
          'GCGTAAGA' => '13',
          'TCGCCTTA' => '1',
          'AGAGTAGA' => '12',
          'GCTCAGGA' => '4',
          'TTCTGCCT' => '3',
          'GTAGAGAG' => '7',
          'CTCTCTAT' => '10',
          'AAGGAGTA' => '15',
          'CATGCCTA' => '6',
          'TAGATCGC' => '9',
          'TATCCTCT' => '11'
        };
second
$VAR1 = {
          'TCGCCTTA' => '1',
          'AGAGTAGA' => '12',
          'CTAAGCCT' => '16',
          'CCTCTCTG' => '8',
          'AGCGTAGC' => '5',
          'GCGTAAGA' => '13',
          'ACTGCATA' => '14',
          'CTAGTACG' => '2',
          'TATCCTCT' => '11',
          'a' => 1,
          'CATGCCTA' => '6',
          'TAGATCGC' => '9',
          'CTCTCTAT' => '10',
          'AAGGAGTA' => '15',
          'GTAGAGAG' => '7',
          'TTCTGCCT' => '3',
          'GCTCAGGA' => '4'
        };
Use of uninitialized value in numeric comparison (<=>) at 1194053.pl l
+ine 66.
Use of uninitialized value in numeric comparison (<=>) at 1194053.pl l
+ine 66.
Use of uninitialized value in numeric comparison (<=>) at 1194053.pl l
+ine 66.
Use of uninitialized value in numeric comparison (<=>) at 1194053.pl l
+ine 66.
Use of uninitialized value in numeric comparison (<=>) at 1194053.pl l
+ine 66.
Use of uninitialized value in numeric comparison (<=>) at 1194053.pl l
+ine 66.
Use of uninitialized value in numeric comparison (<=>) at 1194053.pl l
+ine 66.
Use of uninitialized value in numeric comparison (<=>) at 1194053.pl l
+ine 66.

[download]
Notice the inclusion of use Data::Dumper; and print Dumper($indexfile);. Notice how in the second pass $indexfile has a "short key". I suspect that if you make the same mods to your program you will also notice a "short key". a short key bypasses for(my $k=0; $k<length($key)-1; $k++){ and so $count remains undef.

edit to add: an empty $queryseq also could produce the same kind of result.

In reply to Re: Help with function, count matches and store in hash & retrieve sorted by huck
in thread Help with function, count matches and store in hash & retrieve sorted by Pathogenomix

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