As our 'hero' enters the subway train, ( thirty seconds into the pilot episode ) the carriage has already stopped and he walks through the turnstiles and straight onto the train. Without waiting, or any other pedestrians boarding his carriage. Later, whilst viewing the transit video footage. We are shown that our hero first loitered ( examining his watch - there are no pedestrians in sight ) Then we cut to a close up, where he's suddenly queuing, with other three pedestrians behind him, and the train still entering the station. By the incoming train's windows... this is how our hero is recognised, from the train door reflections. These two scenes, contradict one another.
Detective Martinez's seat belt spontaneously buckles just before her "drive of shame".
In a flashback to World War II, Henry's wife introduces him to an orphaned baby with a number tattooed on his arm, whom the flash-forward identifies as Henry's friend Abe. The Nazis didn't tattoo babies.
When Henry thinks about running away, he suggests to move to Brussels (Belgium) and ask Abe about his Dutch (Abe: a bit rusty). However although Brussels officially is bilingual, most speak French, so Henry could better ask for Abe's knowledge on French. Even so, the Dutch spoken in Brussels is actually Flemish (Vlaams) rather than Dutch (Nederlands) although these two languages are very close.
As our 'hero' enters the subway train, ( thirty seconds into the pilot episode ) he uses the turnstile counter-clockwise, a leaving passenger walks into the same turnstile and goes to exit clockwise.
In the pilot, we learn that Dr. Morgan's death always ends up with him alive and completely naked in water. Aside from his initial murder, we always see him emerge completely naked from the river next to the bridge. However, in a short commercial, Dr. Morgan comes back alive - wrapped with a towel in a morgue drawer.
The pocket watch carried by Dr. Morgan is a an 18 size hunter-style stem-wind American Watch Company, Waltham pocket watch. Dr. Morgan has been carrying this watch since about 1800, even though this model pocket watch was made in 1880 at the earliest.
During the very first of Henry's flashback, the pistol that the ship's captain fires at Henry, although only briefly shown, clearly appears to be one mid/late 1800s revolver instead of a flintlock pistol. Revolver pistols were not yet available until some decades later than 1814-1815, when Henry was supposedly sailing aboard that ship, as depicted in flashbacks of later episodes.
The subway train crashes because someone poisons the conductor, which is odd: poisoning the motorman (driver) might work, but loss of consciousness should make him release the dead man's handle, stopping the train, so not a very reliable way of causing a crash. Killing the conductor would mean only that the doors would not open at the next station.
Morgan is on the train, it crashes, and he is sent to the water, where he emerges naked and is subsequently arrested by two NYPD officers. He is later shown walking out of the NYPD detention center. In the subsequent investigation where he is a suspect this is completely overlooked. It would have eliminated him as a suspect since he would not have had enough time to get from the train crash to the river where he was arrested. Since he was seen on the video security at the train before the crash, this would have raised additional questions as to how he could be in two places at once.
After "Adam" calls, Henry wants to leave for fear of being caught. "I've had every ounce of my blood drain, my organs dissected, all in the name of science." But this couldn't have happened, since his body disappears as soon as he dies.
Dr. Morgan has lived 200 years and is a bit of a genius, yet he never thought about leaving some hidden clothing near the river where he is always climbing out naked.