Missing commands in MySQL command line history
There is an option to prevent some commands that contain specific words from being logged. One common practice is not to log commands that has the word password. 

This option is called histignore 

More info:

https://dev.mysql.com/doc/refman/5.7/en/mysql-command-options.html#option_mysql_histignore
https://dev.mysql.com/doc/refman/5.7/en/mysql-logging.html