Plot hole: In this movie Goblin was able to sneak up on Peter. But in the previous movies Peter was able to sense danger from quite a distance away; Green Goblin from a few blocks and the train barricade from over a mile.
Plot hole: Since they took down the telephone network, it would have been impossible for Justin Long to even be speaking to the emergency response woman for the car, much less send a signal to start the car up.
Suggested correction: Is it possible this is a satellite phone call akin to Onstar?
No, the BMW system requires a cell signal to work, which was taken down earlier in the movie.
Plot hole: The admiral receives the news of the stolen aircraft from the general over an open radio, with umpteen enlisted personnel within earshot. However, when the air group commander asks what the OP is about, the admiral tells him that it is on a need-to-know basis.
Plot hole: The idea that Ben Gates had to run away despite the President's being okay with the kidnapping does not make sense. The President could simply pardon him if necessary. However, when he ran away, he would likely be committing other crimes (fleeing and eluding police, reckless driving, etc.) that would not be federal crimes and so would not be pardonable.
Suggested correction: That's basically what he did at the end. Even though the President was OK with Ben "kidnapping" him, if Ben didn't find the lost city of gold he would have been arrested and charged for kidnapping the President (amongst other charges). However, because Ben was able to find the city the President gave him and his crew a full pardon and explained that it was a misunderstanding.
Plot hole: Spoiler! We find out that "Rogue" is actually Tom Lone, who killed the real Rogue and destroyed his face to prevent identification, then had plastic surgery and went underground to get revenge. But how is the body never identified? Lone was a cop, they'd have blood type, DNA etc. on file, which would have proved the body wasn't his.
Plot hole: Landy uses the code 4/15/71 to point Bourne to the training site address. But how does he know it is on the East side?
Plot hole: When Agent Memphis is about to be executed they ask him if he needs to "Piss" so as to not have government-used drugs in his system before he commits suicide. They even mention writing a suicide note for him. He's had seven shades beaten out of him though and was kidnapped whilst on the phone, mid-conversation and with possible witnesses. Surely if it wasn't the first time they had done this then they would have taken more care to make sure it wasn't a complete fake-out.
Plot hole: In the scene where 47 swings out of the hotel window, we see the booby trap starting to explode as he's still in the room. Then in the shot from outside, the explosion extends out the window - so how on Earth did he outrun it and get out completely unscathed?
Plot hole: I can somewhat understand that in a kiddies' show all aliens can inexplicably speak English - but using Terranean (i.e.: Arabian) numbers as well? While Tetrax's computer uses alien runes, the readout on Gluto's holographic HUDs use Arabic numbers - somewhat a bit too deliberate a producer choice to emphasize intergalactic communication.