Pagination functions won’t work

Don’t create a new query. You can use pre_get_posts for this type of works.

Example : If you want to add books and movies custom post type to home page main loop,

function books_movies_cpt_in_home($query) {
  if ($query->is_home() && $query->is_main_query()) {
    $query->set('post_type', array('books','movies'));
  }
}

add_action('pre_get_posts', 'books_movies_cpt_in_home');