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?
Answer: In the time line of Season 4, William Bell is trying to destroy both universes to create a new one, and he needs Olivia to power the collapse. So he helped her escape. But the real question is, if not in search of Peter, why Olivia has to travel to the alternate universe to be captured and replaced?
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