According to @fuxia comment:
Solution is removing jQuery included by WordPress just before register/enqueue custom jQuery (see https://stackoverflow.com/a/27048128).
So if you include some jQuery on your own, then add
wp_dequeue_script('jquery');
wp_deregister_script('jquery');
just before register/enqueue custom jQuery script in wp_enqueue_scripts action.
Or if you want jQuery included by WordPress just remember, that it’s in no-conflict mode and $ is undefined.
See https://wordpress.stackexchange.com/a/2896/182809 for more details.