Why does Rachel have the Phoenix symbol over her eye when she uses her powers?
It’s never been explained. There’s been plenty of speculation about why, and any explanation now will probably be different from what Claremont was originally planning to do before Ed Brubaker took over writing Uncanny. Ray was first shown with the Phoenix symbol energy signature after she was rescued from being imprisoned by Elias Bogan in X-Treme X-Men 44. Some of theorized that something Bogan did to Ray caused in the Phoenix energy signature. It is also similar to the Phoenix energy signature that Jean had during Uncanny X-Men 381 – 387, and Psylocke’s Crimson Dawn mark. The later has led to speculation that it’s due to some sort of power link between Psylocke and Rachel, which may have been something Claremont was wanting to further explore but never had the chance. In Uncanny 479, the Phoenix energy signature began to glow blue when Ray absorbed the Phoenix Force from the Blade of the Phoenix. That suggests that it is tied to the Phoenix Force and probably was entirely the result