You can explicitly have a join like this:
$qb->innerJoin('c.phones', 'p', Join::ON, 'c.id = p.customerId');
But you need to use the namespace of the class Join from doctrine:
use Doctrine\ORM\Query\Expr\Join;
Or if you prefere like that:
$qb->innerJoin('c.phones', 'p', Doctrine\ORM\Query\Expr\Join::ON, 'c.id = p.customerId');
Otherwise, Join class won't be detected and your script will crash...
Here the constructor of the innerJoin method:
public function innerJoin($join, $alias, $conditionType = null, $condition = null);
You can find other possibilities (not just join "ON", but also "WITH", etc...) here: http://docs.doctrine-project.org/en/2.0.x/reference/query-builder.html#the-expr-class
EDIT
Think it should be:
$qb->select('c')
->innerJoin('c.phones', 'p', Join::ON, 'c.id = p.customerId')
->where('c.username = :username')
->andWhere('p.phone = :phone');
$qb->setParameters(array(
'username' => $username,
'phone' => $phone->getPhone(),
));
Otherwise I think you are performing a mix of ON and WITH, perhaps the problem.