Fauxlivia, having never been experimented on as a child with Cortexiphan, isn't able to open the door between universes, yet does so anyway, and survives crossing over, also impossible for her..
When Olivia dyes her hair brown, it looks wet and wavy but when Charlie comes to her door a few minutes later, her hair looks perfectly dry and straight.
While Peter and Walter are inside the Orpheum Theater setting up the device to get them back to their universe, Olivia & William Bell are under attack from the alternate Fringe Division. Olivia is wearing a red tee under her jacket while Fauxlivia's is white. Even though it is Fauxlivia that crosses over, she is actually wearing Olivia's red shirt.
The police cars in the parallel universe are using the US-style sirens instead of the European-style siren, that are used "over there"
During the final gun fight, Oliva runs out of ammo but her pistol slide still recoils as she pulls the trigger twice.
A camera hanging on a wire is visible on the windows reflection during a traveling shot of New York skyscrapers.