Wp-CLI not working with WordPress installed with composer

If you are calling WP-CLI from the parent directory you need to tell it where core is using --path

$ wp --path=path/to/core

Some more details here: http://wp-cli.org/config/

You can set also set this with a config file wp-cli.yml that contains

path: path/to/core

Details: http://wp-cli.org/config/#config-files