From what I understand, you're wanting to set the tariff_diff  to 1 only if  more than one of the rows that are prefixed with Kuta,DPS50. exist. Matching  on Kuta,DPS50.06, Kuta,DPS50.07, Kuta,DPS50.08, Kuta,DPS50.09, Kuta,DPS50.10.
Assuming all of your records are formatted like: XXX,xxx.###. You can use SUBSTRING_INDEX to parse the prefixed text (Kuta,DPS50.) to use as an identifier.
Then you can use a derived JOIN to match the codes that have duplicates of the prefixed values and update the matching rows.
If there are no duplicate values, no update will occur.
Example: http://sqlfiddle.com/#!9/658034/1 (I added an additional entry for Petang,DPS50.02 to demonstrate it works on other prefixed values.)
Query:
UPDATE mytable AS p
JOIN (
   SELECT SUBSTRING_INDEX(code, '.', 1) AS prefix_code
   FROM mytable
   GROUP BY prefix_code 
   HAVING COUNT(prefix_code) > 1
) AS c
ON c.prefix_code = SUBSTRING_INDEX(p.code, '.', 1)
SET p.tariff_diff = 1;
Result:
|                  code | tariff_diff |
|-----------------------|-------------|
|   Abiansemal,DPS50.02 |           0 |
|         Kuta,DPS50.06 |           1 |
|         Kuta,DPS50.07 |           1 |
|         Kuta,DPS50.08 |           1 |
|         Kuta,DPS50.09 |           1 |
|         Kuta,DPS50.10 |           1 |
| Kuta Selatan,DPS50.05 |           0 |
|  Kuta Ultara,DPS50.04 |           0 |
|       Mengwi,DPS50.01 |           0 |
|       Petang,DPS50.02 |           1 |
|       Petang,DPS50.03 |           1 |
This will also avoid the SQL Error (1093) https://dev.mysql.com/doc/refman/5.6/en/update.html
You cannot update a table and select from the same table in a subquery.