In the scene with Rogue sitting on the bench at the academy (after being stabbed by Wolverine), Bobby come up and tells her to leave. She turns around and you hear her say "Bobby", but if you look closely (it might help to turn the volume down), you can tell that she actually says "Scott". My guess is that they had originally planned on having Cyclops (Scott Summers) tell her to split, but they wanted people to know that it was Mystique. So, they thought of the eye change thing. Now, if it were Scott, he'd be wearing his glasses, so... substitute Bobby.