The architect places a building silhouette over his coffee as the quake intensifies, but in the shot from below and following, there is no cover on the coffee mug.
In the opening scene the location identifier text is spelled as "Manhatan". However, this not a goof, the scene takes place in the alternate universe. This spelling is consistently used 'over there'.
Wire visible to make the metal sculpture move during the opening scene's earthquake.
When they are injecting the cortexiphan in Olivia, Walter says to Peter to turn the monitor, which seems to be ViewSonic. However, ViewSonic was founded in 1987, while the building was closed in 1985 and the monitor couldn't be ViewSonic.
The Jacksonville centre has supposedly been shut down and cut off for years...yet it has a perfectly functioning electricity supply.
When grown up Olive meets her past in the forest and embraces her you can clearly see that the child Olive has blue eyes yet the grown up Olive as we know it has green.