User blog comment:Aithusa07/List of Plotholes from Merlin/@comment-76.9.72.16-20130717205727/@comment-5674726-20130717211433

I think you may be thinking of "The Mark of Nimueh"; Morgana told Merlin that she knew what he did and that his secret was safe but, while he thought that she had seen him use magic, she was actually referring to him being in love with Guinevere.