OS: centos 6.3
DB: 5.5.14
测试创建yoon测试表，没有主键，没有索引，基础数据内容如下：
mysql> select * from yoon;
+----+----------+------+
| id | name | user |
+----+----------+------+
| 1 | ""##!aa | NULL |
| 2 | z2 | NULL |
| 3 | z3 | NULL |
| 4 | z4 | NULL |
| 5 | z5 | NULL |
+----+----------+------+
5 rows in set (0.00 sec)
测试通过一条命令将id设为自增主键，命令alter table yoon add constraint auto_increment primary key yoon(id);创建成功，但是插入2条数据发现报错，场景如下：
mysql> desc yoon;
+-------+-------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+-------+-------------+------+-----+---------+-------+
| id | int(11) | NO | | 0 | |
| name | varchar(20) | YES | | NULL | |
| user | varchar(20) | YES | | NULL | |
+-------+-------------+------+-----+---------+-------+
3 rows in set (0.01 sec)
mysql> select * from yoon;
+----+----------+------+
| id | name | user |
+----+----------+------+
| 1 | ""##!aa | NULL |
| 2 | z2 | NULL |
| 3 | z3 | NULL |
| 4 | z4 | NULL |
| 5 | z5 | NULL |
+----+----------+------+
5 rows in set (0.00 sec)
mysql> show index from yoon;
Empty set (0.00 sec)
mysql> alter table yoon add constraint auto_increment primary key yoon(id);
Query OK, 0 rows affected (0.29 sec)
Records: 0 Duplicates: 0 Warnings: 0
mysql> show index from yoon;
+-------+------------+----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------+
| Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | Index_comment |
+-------+------------+----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------+
| yoon | 0 | PRIMARY | 1 | id | A | 6 | NULL | NULL | | BTREE | | |
+-------+------------+----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------+
1 row in set (0.01 sec)
mysql> insert into yoon(name,user) values ('z','HHH');
Query OK, 1 row affected (0.02 sec)
mysql> select * from yoon;
+----+----------+------+
| id | name | user |
+----+----------+------+
| 0 | z | HHH |
| 1 | ""##!aa | NULL |
| 2 | z2 | NULL |
| 3 | z3 | NULL |
| 4 | z4 | NULL |
| 5 | z5 | NULL |
+----+----------+------+
6 rows in set (0.01 sec)
mysql> insert into yoon(name,user) values ('z6','HHH');
ERROR 1062 (23000): Duplicate entry '0' for key 'PRIMARY'
mysql> delete from yoon where id=0;
Query OK, 1 row affected (0.01 sec)
mysql> show index from yoon;
+-------+------------+----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------+
| Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | Index_comment |
+-------+------------+----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------+
| yoon | 0 | PRIMARY | 1 | id | A | 6 | NULL | NULL | | BTREE | | |
+-------+------------+----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------+
1 row in set (0.00 sec)
mysql> select * from yoon;
+----+----------+------+
| id | name | user |
+----+----------+------+
| 1 | ""##!aa | NULL |
| 2 | z2 | NULL |
| 3 | z3 | NULL |
| 4 | z4 | NULL |
| 5 | z5 | NULL |
+----+----------+------+
5 rows in set (0.00 sec)
mysql> alter table yoon modify column id int auto_increment;
Query OK, 5 rows affected (0.03 sec)
Records: 5 Duplicates: 0 Warnings: 0
mysql> select * from yoon;
+----+----------+------+
| id | name | user |
+----+----------+------+
| 1 | ""##!aa | NULL |
| 2 | z2 | NULL |
| 3 | z3 | NULL |
| 4 | z4 | NULL |
| 5 | z5 | NULL |
| 6 | z6 | HHH |
+----+----------+------+
6 rows in set (0.00 sec)
总结：主要原因alter语法使用不正确，有时候不报错，并不代表命令正确。具体语法如下：
http://dev.mysql.com/doc/refman/5.0/en/alter-table.html