Factual error: In the movie Burke states that none of the computers has a floppy disk drive so that no information can be copied and smuggled out, but Leila uses a USB device. With all their technology and computer scientists, the CIA, or anyone who is semi-computer knowledgeable should know that information can be copied through the USB port and they would have been secured accordingly.
Factual error: Burke says Clayton graduated "top of your class at MIT, majored in nonlinear cryptography..." but MIT has no such major. In fact, there's no such field.
Continuity mistake: When Layla's VW has hit the tree, James's truck is pulled up alongside her, facing forwards. When James drives off, his truck is facing the other way but there was not enough time for him to turn around, or any indication that he did turn around (i.e. no sound of a vehicle making a three point turn).
Factual error: In the middle of the film, as Farrel and Pacino talk in the park, Pacino tells Farrel about a new computer virus that Langley's created. He says it uses existing wires to propagate itself and can spread through, say, an electrical wall outlet. Computer viruses are programs that copy themselves (spread) when executed - this requires specific operating systems and CPUs. Anybody even remotely knowledgeable about computers knows this. The thought that a computer virus could somehow spread through the electrical grid or infect a toaster is ridiculous, since the only part of a computer actually connected to the electrical net is the PSU, and no data goes from it to the CPU.