User blog comment:ArthurMerlinLancelot/FINALLY/@comment-5684105-20121216072859/@comment-4879894-20121216191437

In the 2.02, Merlin couldn't tell Morgana the truth as he thought that she already knew it. Morgana  didn't know that she was the vessel of the spell and Merlin didn't know that she didn't know. A huge misunderstanding ! That's why Morgana, in the first place, didn't understand why Merlin poisoned her.