I will say as a whole this issue had many holes in the plot but maybe that was intended who's to say.
My theory is that Wanda was somehow resurrected through the protocols. The Wanda we see at the end, is the old backup they've talked about. So that's why she goes to kiss Vision as if they were still together.
The current Wanda, which we see as a "spirit" or whatever in issue #1 and one page of this issue is still dead, though in the process of getting resurrected/resurrecting herself. That's why the solicits of issue #4 say "A Wanda divided cannot stand", while having a cover that shows one/two Wandas coming out of another.
Vision and Wanda is like if Pinocchio and the fairy god mother hooked up
Magneto: None of you knew what was Home for Wanda
Quicksilver: Hello??? Her only and twin brother who literally lived with her standing right here???
Just to add some depth and history to the scene between Jean and Vision in this issue, from Avengers #110 (1973):
I think “Trail of Magneto” will explore what Resurrection looks like “On the Other Side”.