Factual error: When they show the fact sheet for Dr. Bishop, his license is marked revoked, yet the license in the picture was not around when Dr. Bishop was locked up.

Plot hole: The contagion used on Flight 627 was apparently so contagious that every passenger became infected in seconds. However, when John is infected with the contagion, Olivia, Peter, Walter, and the other doctors are able to tend to to him without getting infected.

Factual error: When the 747-aircraft of the fake German airline is being shown, you can see the German flag on the plane. But you also see an "N-xxxxx" registration which stands for USA. If it were a real German plane, it would have a "D-xxxx" registration.

Plot hole: When Dr. Bishop is using the special camera to capture the images on the dead woman's retina, he tells everyone to put on their goggles to protect them from the flashes. Once they find the image they need, everyone takes off their goggles, yet the camera is still flashing, and there are no ill effects.