Query entity backend SQL script.

As far as I know you will be able to see them in logs. But you need to customize them with logger level as DEBUG or INFO. Refer -
docs.appian.com/.../Customizing_Application_Logging.html

But just to understand more on your problem -
1) Are you using any view to fetch data using qe and do you have any sorting in the view?
2) Are you using in clause as in clause will return resultset in different order?
3) Do you get different rows in both scenarios or is it only sorting that is differed?

Approach 1: Please check the below URL to log the details of Write to Data Store smart services and Query Rules.
docs.appian.com/.../Customizing_Application_Logging.html

Approach 2: If still you are not able to see the SQL query being executed when you use the QE. Then follow the below steps.
1. Log in to your MYSQL console or client.
2. Select the database where the queried tables exist.
3. Put a lock on the table being queried using the below command.
LOCK TABLES tablename READ;
4. Execute the below command to see all the queries being executed on the database and identify yours.
SHOW FULL PROCESSLIST;
5. Unlock the table using the below command.
UNLOCK TABLES;

NOTE: Use the 2nd approach only if the 1st approach doesnt suffice your requirement.

Hope this helps.

Regards,
Sidhant Behura