The positions of the "frozen" bus passengers change between the shot of the police officer discovering them and the subsequent scene of the main characters investigating the scene. Most obviously, the dead DEA agent disappears from her frozen position between the two scenes.
(at around 17 mins) While Charlie is talking to Olivia, a crime scene woman walks through the door behind Charlie. When the camera angle changes a second or two later, the woman is nowhere to be seen.
When Davidson cuts Evelina's palm open with the scalpel, the blade is actually facing away from her hand.
The drugs Walter is "self medicating" with, while having the small potential to cause psychosis if abused, are not classified as psychotics and are actually all commonly prescribed medications. Dextromethorphan is a OTC cough suppressant and is the active ingredient in most over-the-counter cough syrups. Clonazepam (Klonopin) is a benzodiazepine commonly used to prevent seizures and panic attacks. Fluoxetine (Prozac) is a SSRI-class antidepressant.
A computer readout for a DEA employee reads "Drug Enforcement Agency" when in fact "DEA" stands for "Drug Enforcement Administration".
At Agent Scott's funeral, the flag is shown draped with union over the right upper corner of the casket, but it should be over the left front, or the heart.
Walter wanted Mass in A Minor by Bach played but there are non written in that key. B minor, sure, but no A Minor.
When Walter is showing the puzzle pictures in the lab, he does so with a video projector, which is obvious from the rapid changing of the highlighted demonstration slides of the rabbit/duck image without a phase of black in between them; the sound however the machine makes each time Astrid clicks on the remote is the one of an old slide projector, mixed with a rather uncommon beeping sound.
The final confrontation is supposed to take place at South Station, which is a real transit hub in Boston. However, the building shown is considerably smaller and different in architectural style from South Station.
One scene supposedly takes place at Boston College, but the establishing shot shows a building which is of a different architectural style from Boston College and the neighborhood which Olivia is shown driving through looks nothing like the neighborhoods around Boston College.