When the X-Man trade was being released, it was advertised as "Nate must confront the woman who might be his lover Madelyne, his mother Jean, if not both!" Nate, before he became a shaman, hung out with Scott and Jean in Alaska and got to know them better. When Cyclops saved Nate from Apocalyse, Nate even called Cyclops family. He was like 'why'd you do that man, we're family and because of that Apocalyse can use your body as well." Nate was just in the process of putting himself together and was very disoriented. I can see him being fooled.