phpMyAdmin showing database is MyISAM but tables are InnoDB
Databases don't have storage engines, only tables do. I have no idea what PhpMyAdmin is trying to indicate there, perhaps the system-wide default engine or something. The documentation would presumably shed some light on WTF is going on.
This is not a bug. From the MySQL documentation:
A database may contain tables of different types. That is, tables need not all be created with the same storage engine.
So you're fine.
To see the table type:
SHOW CREATE TABLE schema_migration
To see the database storage engine:
mysqldump --no-data $YOURDATABASE