@ORM\Id means values of this field MUST be unique. With the boolean type they can be unique only in 2 or less row (because boolean has only 2 values - 0 and 1). I think you have logical mistake, and must simply change type of field to integer. Like that:
/**
* @var integer
*
* @ORM\Column(name="machine_id", type="integer")
* @ORM\Id
* @ORM\GeneratedValue(strategy="IDENTITY")
*/
private $machineId;
Then update your schema by ./app/console doctrine:schema:update then recreate data into table.