Since your entities are related, you should use JOIN
instead of multiple SELECT
s:
$repository = $this->getDoctrine()->getRepository('jwatchBundle:Appuser');
$query = $repository->createQueryBuilder('u')
->join('u.watches', 'w')
->where('w.id IN :watched_ids')
->setParameter('watched_ids', array(1, 3, 12))
->getQuery();
$result = $query->getResult();