User blog comment:ArthurMerlinLancelot/FINALLY/@comment-5684105-20121216072859/@comment-5674726-20121217000410

Morgana DID know in 2.02 why Merlin had poisoned her.

She couldn't have known in 2.12. She was asleep when Morgause enchanted her and knew virtually nothing about magic at the time. Merlin needed Kilgharrah to tell him that the sleeping spell was such powerful magic that it required a living host. Morgana couldn't be expected to know the limitations of magic, or to deduce that she was the source of the spell. To the best of her knowledge, her magic was protecting her from the effects of the sleeping spell.

Maybe Morgause told her that she was the source of the spell at a later date but, even if she did, Morgana wouldn't credit Merlin with being able to figure out that she was the source of the spell. I'd say that, from her perspective, Merlin knew she had magic and knew or guessed that she was working with Morgause, and he poisoned her so he could use her life as a bargaining chip to get Morgause to call off the Knights of Medhir.