At about 28 minutes in when David Robert Jones walks up the steps to meet Colonel Broyles, there is an observer just behind David who passes him.
While listening to the satellite transmissions from the plane. JFK Airport is still known as Idlewild.
The glyphs for this episode spell out: SIMON
Another difference between the two universes, Sherlock Holmes is unknown or at least not widely known in the USA.
The opening scene is set in a business called Artz Holdings, a nod to the stock character, Dr. Leslie Arzt (Daniel Roebuck), from LOST, another JJ Abrams series.