Will pulls and releases the slide on his semi-automatic pistol twice (once in the lavatory and once outside the uncle's flat), after he's already fired it in earlier scenes. This would have ejected a round already in the chamber.
Will and his dad Martin drive to an apartment to get a gun, they park the car that looks like a Seat MPV or something with 7075 GXF on the license plate. They get out and drive the same car away, but when they arrive to meet Jean Carrack, the car is an Audi SUV with 1892 GXA on the plate, after apparently switching cars at Tom/Martin's apartment.
When Will and Lucia are travelling by train to Puerta del Sol, Lucia is wearing a blue jacket. When she says goodbye to Will in the train station, the jacket is gone. Lucia is neither wearing nor holding it, nor does she have it tied around her waist.
When a boat drops the anchor there is no need to steer.... the rudder only works if the boat actually moves. Just like a car.
Will never runs out of bullets and has no magazines.
Carrack's SUV slides to a stop balancing precariously with the front over the stairs going to the subway. When she gets out of the front, the front suddenly becomes heavier WITHOUT her weight, causing the SUV to tip into the stairwell and slide down the steps. An interesting lesson in how physics does NOT work! Obviously, the SUV was secured when Sigourney Weaver was in it. But with her out of the SUV (which would have made the SUV more secure as its center of gravity moved toward the back, and away from the stairwell) it was then pulled/pushed into and down the stairwell for dramatic effect.
Will is very active and agile for someone with a bullet hole in their back. Of course anyone actually shot would have needed quite a bit of time of bed-rest in order to recover from such trauma. Not the few hours Will needed.
Lucia goes down on her bike. Though she is wearing a dress and lays the bike so that the left side of her bare left leg hits the road, she leaves no skin on the road and does NOT bleed.
In Puerta del Sol, there is a large Audi advertisement on the side of a building. Though it says in big letters "hola", the smaller writing says "Audi A1...The next big Audi". If this advertisement truly were in a Spanish city then "The next big Audi" would have been in Spanish in order to sell Audis to a Spanish speaking market. Clearly this advertisement was in actuality geared not to the Spanish speaking market of Puerta del Sol, but to an English speaking MOVIE VIEWING audience in the US.
Will is shot and Lucia takes him to a friend who is in medical school. The medical student looks at the wound. Will's back is bloodied from the entry would, but there is no blood on his stomach indicating that as there is no exit wound, the bullet must still be in him. But this medical student says there is no bullet? If the bullet entered and traveled through Will, there would be an exit wound. But if there is no exit wound, then the bullet has to still be in Will.
When Will and Lucia fall whilst on the motorcycle, if you look carefully you can see that the latter's stunt double is wearing noticeable leg-padding.
When Will (Henry Cavill) gets back on the boat in the Beginning of the movie to find no one is on the boat, he looks into a cubby with a mirror with his reflection. You see him for sure on the top right, before the switch, you see the camera person hands and wires 00:15:39-00:15:40.