Summary:

Check if query is not blocked by another one

Use SHOW PROCESSLIST

Use SHOW ENGINE INNODB STATUS to get information about transactions which use InnoDB tables.

Analyze wrong result and solve the problem using result of analysis.

Below I place list of methods which we studied in the second part.

Method #11: use query SHOW PROCESSLIST to see list of queries which run at the same time.

Method #12: use table INFORMATION_SCHEMA.PROCESSLIST if you need list of simultaneous queries ordered by one of parameters.

Mehtod #13: use query SHOW ENGINE INNODB STATUS to get information about transactions.

Method #14: use general query log if output of SHOW ENGINE INNODB STATUS contains only part of information about problem transaction.