Parece que log_queries_not_using_indexes
está ativado.
Verifique fazendo:
mysql> show global variables like 'log_queries%';
+-------------------------------+-------+
| Variable_name | Value |
+-------------------------------+-------+
| log_queries_not_using_indexes | ON |
+-------------------------------+-------+
Desligue com:
mysql> set global log_queries_not_using_indexes = 'off';
Query OK, 0 rows affected (0.00 sec)