In Which We Meet Mr. Jones - S1-E7
Deliberate mistake: Dunham comments that she works for Homeland Security. While the FBI is under the jurisdiction of the Justice Department, she works as part of a special Homeland Security task force; so saying she works for DHS is an accurate statement.
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?
AmiSecured