When Booker arrives to rescue Duncan, he's seated on the driver's side of the car. In the next scene, he's returning fire from the passenger's side of the car.
When Booker goes to rescue Duncan, he fires groups of 5 - 6 bullets several times from his ordinary service pistol without ever reloading once.
While Penny attempts to hack the traffic light computer remotely from Booker's car, the scene where they cross the intersection with the red light is shown three times.
When Booker and Penny go to rescue Duncan, Booker tells Penny to disable the lights and she is seen frantically typing into the laptop. However it's clearly shown that the laptop screen, despite being illuminated, is actually blank.