I am afraid that this is standard MySQL behaviour. The DBI will report whatever it gets from the DBD driver, and in this case MySQL does not report the table name.

mysql> describe test;
+-------+----------+------+-----+---------+----------------+
| Field | Type     | Null | Key | Default | Extra          |
+-------+----------+------+-----+---------+----------------+
| id    | int(11)  |      | PRI | NULL    | auto_increment |
| title | char(10) | YES  |     | NULL    |                |
+-------+----------+------+-----+---------+----------------+
2 rows in set (0.00 sec)

mysql> select * from test;
+----+--------+
| id | title  |
+----+--------+
|  1 | first  |
|  2 | second |
+----+--------+
2 rows in set (0.00 sec)

mysql> select a.id, a.title, b.id, b.title from test a, test b where a
+.id=b.id;
+----+--------+----+--------+
| id | title  | id | title  |
+----+--------+----+--------+
|  1 | first  |  1 | first  |
|  2 | second |  2 | second |
+----+--------+----+--------+
2 rows in set (0.00 sec)
[download]

As you can see, querying from the normal MySQL client, the server is returning the same name for both fields. Thus, DBI will get only one of the two columns.
From DBI POD:
If more than one field has the same name, there will only be one entry in the returned hash for those fields.

However, if you ask esplicitly, you get the distinction.
I advise you to differenciate ambiguous names ALWAYS, no matter how smart the database driver seems to be .

mysql> select a.id as a_id, a.title as a_title, b.id as b_id, b.title 
+as b_title from test a inner join test2 b using(id);
+------+---------+------+---------+
| a_id | a_title | b_id | b_title |
+------+---------+------+---------+
|    1 | first   |    1 | first   |
|    2 | second  |    2 | second  |
+------+---------+------+---------+
2 rows in set (0.00 sec)
[download]

 _  _ _  _  
(_|| | |(_|><
 _|
[download]