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.
Plot hole: When interrogating Boone, Olivia shows him a photo of a body with the spine torn out in the woods. This body hasn't been found yet, as a later scene has Olivia and Peter go to the same location and find the body. You can tell it's the same body because the shirt is the same in both the picture and the crime scene.
Plot hole: When Charlie looks up the file on David Esterbrook, he says that the file shows that Esterbrook is directly responsible for INtREPUS' "controversial" R&D, including pre-natal gene therapy, human/animal hybridization, and viral warfare. Yet later, Olivia says she can find no dirt on Esterbrook who is, in her words, "cleaner than snow". If INtREPUS kept records of their illegal endeavours, then how come Olivia can't find them when the time calls for it?