Plot hole: The very ending scene where Peter (in this version died in the ice as a boy so Walter's wife never met him) takes off some of the dust covers then picks up a toy airplane. The toy airplane he got as a child from ... Walter's wife when she was trying to placate him in an earlier episode for trying to run "home". This toy airplane wouldn't have been his as a child in this version of the universe. (00:42:00)
Phillip Broyles: Someone out there is experimenting, only the whole world is their lab.
Question: In the original timeline, when Fauxlivia and our Olivia are in their opposite universes, the thing that makes our Olivia remember her real life and try to escape is the memory of Peter. In the new timeline, he doesn't exist. When Walternate has found and synthesised the Cortexiphan, he says that our Olivia is no longer necessary and to kill her. How did she get back to our universe with no memories of Peter, and no alternate Broyles helping her to escape and being sent to us dead with one leg?