In Fringe's season 1, the episode The Transformation (1x13) shows how Marshall Bowman travels on VertusAir flight 718. We witness how he develops some strange symptoms, withdraws into a lavatory and transforms into a porcupine-like monster.
At the end of season 3, Peter "switches" the timeline (changing the past and making the present continue in a different timeline henceforth) from blue- to orange-verse. Various statements throughout the 4th season indicate time (the date) was not reset; Olivia and Walter have been working on Fringe cases for some three years etc. - hence it is safe to say that season 4 plays 3 years after season 1.
Then, in the episode Nothing As It Seems (4x16), the events from 1x13 happen again, up to the point of Bowman's transformation, which this time doesn't happen (not aboard the plane, anyway). As far as I can tell, great care was taken to exactly recreate the events from the season 1 episode, including hiring the same actors to play the flight attendants once again (Olivia Palenstein and Mike Realba), so obviously this is supposed to be the same event with slight changes.
Peter, as well as Olivia - who is in the process of regaining her memories from the blue-verse -, remember the events from 1x13 and note the difference that Bowman's transformation happened later this time, implying that in the orange-verse, everything related to flight 718 played out the same way, except for the small difference that the transformation happened a bit later.
BUT ... all of this happened 3 years later!! Is there any explanation for this?
How unlikely is it that in the orange-verse timeline, Marshall Bowman is on the very same flight with the very same flight attendants 3 years after the same would have happened in the blue-verse? Mind you, this is not a "small change" in the course of events while mostly everything else stays the same.
So, why did Peter and Olivia realize the transformation happened a tad later in the orange-verse timeline, but were not baffled by the fact that essentially the same events as in the blue-verse happened, but three years later?
EDIT: Not only the flight and the flight attendants were the same in both episodes. The passenger next to Bowman was the same, an elderly lady played by Judy Sinclair both times, as well. Moreover, the transcripts of 1x13 and 4x16 reveal that the dialogue between Bowman, the passenger next to him, and the cabin crew is the same down to the lines of text until the moment of transformation.
Interestingly, the announcement by the captain in the beginning seems to be different - starting the inflight movie + selling headsets vs. circling before beginning the final descent + selling snacks. On the other hand, this could be presumed to be a slight retcon, as in 4x16, it was crucial for the plot that the plane would be close to landing, and starting the inflight movie would not make much sense right before landing.