My guess is you need to refresh @store_array within the @first_directory loop

foreach my $first (@first_directory){
  my @store_array = qw (1 2 3 4 5 6); # here
  while(my ($i,$j) = splice(@store_array,0,2)){
    my $second_directory = "$first/$i/$j";
  ..
[download]

try

#!/usr/bin/perl
use strict; use warnings;
use File::Glob 'bsd_glob';

my $store_location = '/path/to/file/store.txt';
open my $fh_log, '>', $store_location
   or die "Fail to open file '$store_location' $!";
  
my $Dir1 = "/somewhere";
my $Dir2 = "/somewhereelse";
my @first_directory = ( $Dir1, $Dir2 );

foreach my $first (@first_directory){
  my @store_array = qw (1 2 3 4 5 6 7 8);
  while (my ($i,$j) = splice(@store_array,0,2)){
    my $second_directory = "$first/$i/$j";
    if (-e $second_directory and -d $second_directory){      
       my @files = bsd_glob("$first/$i/$j/*");    
       foreach my $file (@files){
         my $lines = 0;
         my $match = 0;
         open(FILE, "<" , $file) or die "Can't open file '$file': $!";
+    
         while (<FILE>){
            if (/TbhODK|octuov|qas_uop/) {
              ++$match;
            }
            ++$lines;
         }
         print "$file : $lines lines read. $match matches found\n";
         close FILE;    
         print $fh_log "File $file has $match matches\n";
       }
    } else {                
       print $fh_log "Directory $first/$i/$j (fail to exist)\n"; 
    }
    
  }    
}
close $fh_log;
[download]