MySQL 5.6 performance_schema not showing queries from application
P_S in MySQL versions below 5.7.4 doesn't collect information regarding executed prepared statements: https://dev.mysql.com/doc/relnotes/mysql/5.7/en/news-5-7-4.html.

Maybe your application is using prepared statements instead of simple ad-hoc statements (parameters concatenated). Some client libraries, like PHP's PDO can avoid this (MySQL's) issue by emulating prepared statements in software, instead of sending them to MySQL for preparation (PDO option PDO::ATTR_EMULATE_PREPARES).