Bear with me, but Director Devo - the guy in charge of Orchis - is blind but told Alia Gregor that his machines allow him to see in more ways than he could have as a human. Mystique ran into him when she infiltrated the Orchis Forge. Is it not possible that Devo knew what she was and let her go around the base to figure out what she was doing the first time she passed through and when she left without killing Gregor, realized that there was something wrong. X and Magneto told Mystique to go back in the next day to kill Gregor and while we've got no indication of whether she did or not, the books have clearly advanced past that point in time. If I had to guess, Mystique goes back the next day and is easily suborned by Devo given how angry she already was at X and Magneto and she brings back false proof that she killed Gregor and Nimrod has been stopped.