User blog comment:DragonsHaveMoustaches/Did Morgana see Merlin using magic in 'Another's Sorrow'?/@comment-5253758-20121028222435

Firstly, I think that if she did find out that moment it would be lame... The reveal should be much more epic as Phoenixon said.

To get to the point, I believe that she did not see him using magic as too many things were going on that moment.

The cave was collapsing, her plan was being destroyed and Arhur was escaping. If you watch closely you could see that she was kind of lost. The whole scene took her by surprise. I think (actually I'm pretty sure) that she did not notice him.