Factual error: The villain performs his hit at the beginning of the movie by remotely changing the GPS destination of a cab, so they head to the wrong place and into an ambush. Assuming that neither the cabbie or Pope notice the change on screen, and that his sophisticated software silenced the voice announcement of the course being recalculated, and makes the new place also marked as the old one (it is after all a god-like movie software), the trick is done on on a London black cab, whose drivers are notorious for "The Knowledge", aka being required to learn the entire topografy of the city in one of the most demanding training courses in the world, and not using GPS. It'd be definitely unlikely for the cab driver to be totally unaware, to the point of Pope himself noticing first that they are at the wrong place.
Factual error: Jan Strook is a Dutchman; throughout the movie he is referred to as "Jan Strook", which rhymes with "took," when it should rhyme with "broke." This is even worse considering he has a Dutch accent in the movie, which leaves him no excuse for mispronouncing his own name.
Factual error: When the helicopter arrives at Dover AFB carrying Jericho, the controller states runway 22L. Dover AFB has intersection runways 1/19 and 14/32 and no parallel runways.
Revealing mistake: When Jerico is having his surgery the angle of the device that will be transmitting the memories is inconsistently angled in the real shot versus the monitor image.
Plot hole: Jerico leaves Jill's house to go to the university, driving her car. While he's away, Elsa pays her a visit and extorts the location. When we see Jerico at the university, he enters the book cellar, finds the famous duffel bag almost immediately, and as he exits, outside there's Heimdahl sitting there, having set him a trap. That would already been hard to swallow, but we could assume his location was significantly closer than Jerico's to the university library and Elsa phoned him. But becomes downright impossible when we see that to pull the lever of the Home Alone-ish trap there's none other than Elsa, miraculously arrived at his destination despite him having a huge headstart.
Plot hole: The CIA is desperately trying to find Pope's contact, to the point of doing the crazy experimental brain surgery shipping over the ocean the one scientist that may perform it, and an inmate. But they don't have Pope's house under surveillance or his phone tapped, so they have no idea Strook called him. The fact that Strook not hearing back from Pope would try to contact him was quite literally the most obvious possible event. (00:31:00)
Factual error: The bad guy's henchwoman reads the license plate as "SI52JGN", he repeats it as such but on screen he types "S152JGN" (with the second character as a number 1 and not a letter I). I (like Q and Z) is a letter that can't be used in the first 2 digits of a UK license plate, anyway. (00:04:45)