I am getting the issue:
Integrity constraint violation: 1052 Column 'created_at' in where clause is ambiguous'
but the table
SELECT DISTINCT main_table.*,
blacklist.entity_id AS marked
FROM sales_flat_order_grid AS main_table
LEFT JOIN (SELECT main_table.*
FROM plugincompany_blacklist_item AS main_table
WHERE ( order_id != '0' )
GROUP BY order_id) AS blacklist
ON main_table.entity_id = blacklist.order_id
WHERE ( created_at >= '2016-11-03 00:00:00'
AND created_at <= '2016-11-26 23:59:59' )
Both tables have a created_at clause. So mysql does not know which one to take. You need to be clear about that:
WHERE ( main_table.created_at >= '2016-11-03 00:00:00' AND main_table.created_at <= '2016-11-26 23:59:59' )