Trying to reproduce the issue José was talking about.

TableTest.php

/**
 * Tests that patchEntity includes _joinData
 * all associations
 *
 * @return void
 */
	public function testPatchEntityJoinData() {
		$articles = TableRegistry::get('Articles');
		$articles->belongsToMany('Tags');

		$entity = new \Cake\ORM\Entity;
		$data = [
			'title' => 'testing',
			'tags' => [
				[
					'tag' => 'CakePHP',
					'_joinData' => ['active' => 1]
				],
				[
					'tag' => 'Internet',
					'_joinData' => ['active' => 1]
				],
			]
		];
		$articles->patchEntity($entity, $data);
		$this->assertInstanceOf('Cake\ORM\Entity', $entity->tags[0]->_joinData);
	}