Excluding rows from a query on a combination of mulitple conditions
To be precise, to ...


  remove rows where query_id = 10 and flag = 'IGNORED'


... you need something like this:

SELECT * 
FROM  ...  -- you are hiding a more complex query here!
WHERE (Flag.Query_id = 10 and Flag.query_flag = 'IGNORED') IS NOT TRUE;


In a WHERE clause, only TRUE qualifies. Rows with FALSE or NULL are excluded.

What you display:

...
WHERE NOT (Flag.Query_id = 10 and Flag.query_flag = 'IGNORED');


... would also exclude rows with NULL values in Flag.Query_id or Flag.query_flag - not exactly what you asked for. Even if the columns are defined NOT NULL, NULL values can be introduced with an OUTER JOIN or similar in your undisclosed query.

(The sample rows you display are not affected, since there are no NULL values.)