Plot hole: The secret CIA base at Kamp Woody was underground. Kids searching for years have combed the camp, but never found it, but when Cody is going down the escalator, you can see bright skylights on the roof. If the sun is able to shine through, that means the skylights aren't hidden, and the kids would be able to find the camp.
Plot hole: When Dan is chasing after Carter to catch him and Alex together at the restaurant, there's very little chance he could have had any idea where Carter was going. He couldn't have told the cab driver to "follow that taxi" because in the time between Carter getting in a cab and Dan getting in a cab about 5 taxis drive past, so how he happens to end up at the same place is a miracle.
Plot hole: How does Agent Lahiri know that you needed to raise the pylons before it was possible to make the cross bow shot the boys needed to unlock the house in Amsterdam? Additionally, those pylons would not be accessible through water as they are planted in mud under the foundation of the building, not water.
Plot hole: When Gawain is repairing the hole in the vault wall, a security camera is visible in the top corner in the room.
Plot hole: The Hillbillies take a "short cut" to catch up with the guys after they are taken in by Burt Reynolds. However, the guys get a chance to sleep comfortably until morning before being confronted by them. (01:12:10)
Plot hole: When the students are breaking into ETS, they take great care to avoid the security cameras in the lobby; donning masks, crawling on the ground, etc. Yet a bit later, two of them go back to guard the same lobby, they are seen walking around and sitting on the desk that they so carefully crawled past earlier.
Plot hole: Bridget is wearing a shirt from Mrs. Darcy (the line about Mark's mother's taste in shirts, which is said while showing BOTH shirts, definitely suggests that - her idea of cuteness for a couple, I guess), which doesn't make sense because the first movie ended on New Year's Eve (we know that because Shazzer and the rest of the gang were taking Bridget to Paris that night to celebrate the New Year, but Bridget ended up with Mark - unless the movie take place a year later, which it doesn't, it takes place the next day). Consequently, there is no way Mrs. Darcy would have known about Bridget and Mark in time to get her a shirt too and offer it to her. Mark couldn't have brought it to Bridget, because she arrives alone at her mother's New Year's Day turkey curry buffet; Mark is already there, wearing the shirt his mother gave him, which suggests they split ways that morning, after their first night together.
Plot hole: In the scene where Michael Shannon attempts to rob John C. Reilly and Diego Luna, he takes the briefcase, looking for the check, but it is empty. Diego Luna then reveals he has the check in his pocket. In none of the previous scenes does Diego Luna have a chance to take possession of this check. The check remains in the briefcase, and the briefcase is always in John C. Reilly's possession.
Plot hole: During the sudden death event, Peter and White are told that both feet must remain in the triangle at all times. When Peter throws the ball, his left foot is outside of the triangle.
Plot hole: If Happy Chapman is supposed to be allergic to cats how come he doesn't sneeze whenever he is around Garfield?
Plot hole: Near the end of the film, the crippled Thunderbird 5 is about to catastrophically re-enter the Earth's atmosphere and burn up. Predictably, the younger Tracy brother restores control, saves Thunderbird 5 and all on board. A few seconds later, a computer announces that Thunderbird 5 has resumed a geostationary orbit (such orbits are only possible at an altitude of 400km) My point? Pulling out of a fall, climbing 370km in a few seconds, and then stopping dead 400km up would have required such a massive acceleration/deceleration that everyone on board would probably have been pulverized, even if it were possible for a badly-damaged space station to move that fast.
Plot hole: At the end of the movie when getting out of the bear pit, the crew decides to use a ladder when a set of stairs can be seen. Was this so Vince Vaughn could give his respect speech?
Suggested correction: You forgot to mention the stairs are also in the bear cave and there's no guarantee they lead out of the pit.
Plot hole: When Jo is getting to walk down the aisle with Queen Clarisse, he hands Shades his top hat and then pops his ear piece right off, in a split second, and puts it in the top hat. In the previous scenes, Princess Mia has Lionel's ear piece stretched from the back of his neck, across his jaw and around his chin and then stretched to her ear but it hasn't popped out, while Queen Clarisse jerks Charlotte with her when she goes to listen to Princess Mia.
Plot hole: Max apparently hacked into the Suburban's 'ON STAR' system to take remote control of the vehicle. Not possible: There is no way to shift into drive, steer, apply brakes, or apply the gas pedal by remote control unless there are previously installed mechanical devices that can operate those controls. The electronic controls in a modern vehicle can only operate mechanical devices, and the ones needed to do this type of thing are NOT installed on any car from the factory. It is also clear that Max did NOT somehow previously install these devices on the vehicle unbeknown to Stan, for Lola( dressed as the street bum) had to retrieve the VIN number in order to access the 'ON STAR' programming, which they would have already had if they had previous access to the vehicle.
Plot hole: At the party towards the end of the movie, the 3 babies are crawling around on the floor. There's no way not one person at the party saw them.
Plot hole: The hot air balloon carries Fogg and friends quite a distance, but where is the heat source?
Plot hole: Lucy has been painting pictures of Henry since she moved into the institute. But she passes him at the zoo and doesn't recognize him.
Plot hole: Kahuna seems to be about five or six, yet the formula he took stopped him from aging, even though he was a baby when he took it.