Board Thread:Questions and Answers/@comment-4623180-20120919141837/@comment-12511635-20150528100810

Merlin has a pretty good reason not to trust (or at least to be somewhat uneasy about) Morgana, despite their past relationship. In To Kill the King he sees firsthand that Morgana can be extremely dangerous when crossed, going so far as to appoint herself judge, jury and executioner for Uther (but not going through with it right at the last second). Later in The Nightmare Begins, he not only has the Dragon's warnings about her knocking about in her head, but he witnesses her refusal to return to Camelot despite the fact that a dozen or so innocent lives are at stake.