I cannot remember if she was exactly in phased form, but she was also far less experienced during those days too. Shadowcat was sporting that tacky multi-color costume during the encounter and I believe under the codename name Ariel. But indeed injurying what he classified as a child struck a chord with him and ceased him from the engagement.
Yeah, it said she was in phased form. In fact, they said that was the only thing that saved her life. Given that the crux of her abilities is basically to be phased, if Magneto can hit her phased, it doesn't really matter how experienced she is, unless she uses her powers in ways I've *never* seen her use in combat, such as hiding in walls and sneak attacking Magneto with a quick phase/unphase/heart grab technique or something. But that's pretty out of character for her, and I've never seen her fight that smart.