I think I see what the problem is - in your inner loop, when you find a match you are inserting 'Feature', but you are not exiting that inner loop. Instead, you are continuing in the inner loop to process the next element of @idfeat. Try something like this (untested):

   my $insert_sql = qq{
      INSERT INTO dd
      VALUES(?, ?)
   };
   my $sth_insert=$dbh->prepare($insert_sql);

   for (my $eu=0;$eu<=(scalar(@identifier));$eu++){
      my $match_found = 0;
      foreach my $id(@idfeat) {
         if ($id eq $identifier[$eu]){
             $match_found = 1; # found a match
             last; # break out of the foreach
         }
      }
      if ($match_found) {
          $sth_insert->execute($identifier[$eu], 'Feature');
      } 
      else {
          $sth_insert->execute($identifier[$eu], 'Bug');
      }
   }
   $sth_insert->finish;
[download]

Read up on using 'placeholders' in the excellent DBI documentation by doing

   perldoc DBI
[download]

at a command prompt. Using placeholders will only help you - they take care of all quoting issues (which can be a real pain in the butt), and they can improve performance.

HTH.