The EMP device goes off at the last seconds of the previous hour. Yet among the very first images we see of this hour, there are already paramedics wheeling injured/dead people away and obviously various other action too has somehow taken place in practically zero amount of time.
Jack tells Phil Holden of the NSA that the terrorists got off the Williamsburg Bridge at West Broadway and Roebling Street. The Williamsburg Bridge connects Brooklyn to the east side of lower Manhattan, and whereas Roeblin Street is near the Williamsburg Bridge in Brooklyn, West Broadway is on the west side of Manhattan, nowhere near the bridge. In addition, if the terrorists had gotten off the bridge in Brooklyn, it would mean that they actually left Manhattan, which makes no sense because they were trying to get INTO Manhattan. Also, when the terrorists' vehicle stops near the foot of the "Williamsburg Bridge," they have a full-on view of the Empire State Building, which is considerably further north from that spot in Brooklyn.
The National Security Agency is located in Maryland, not Washington, D.C.