As Harold and Kumar drive Neil Patrick Harris' car through Alabama, the license plates on the car clearly read "Virginia", but for one scene as they enter Texas, the license plates read "Texas". Then, later they are back to "Virginia".
When Harold backs the yellow sports car into the fire hydrant, the hydrant topples over and water gushes everywhere. But in a closeup of the rear of the car a short time later, there is no damage to the car, not even a scratch on the bumper.
In Alabama, when Harold and Kumar are driving down the street toward the pickup basketball game, you can clearly see it raining through the windshield. When the camera cuts back, it is not raining and the street is dry.
When Harold and Kumar are taking the plane back to Guantanamo Bay, they have two agents sitting on each side of them. The agent next to Kumar brings his hand up to his mouth, coughs, and says "Queers!", however, in the next shot the agent's hand is down by his side.
While Harold and Kumar are on the flight to Amsterdam, Harold is watching a movie on his laptop. When they show a shot of Kumar he has a pillow behind his head. They change shots and come back to showing Kumar, where the pillow is different, with a dark blue stripe. Finally, the last shot of Kumar in the sequence the pillow is missing.
At the beginning of the movie, after Kumar opens the bath curtains, they are covering his right shoulder. But in the next shot, when the camera is behind him, they are clearly more open and not covering his body.
When Harold complains about Kumar using the toilet while he is trying to shower, Kumar reminds him that they just ate 30 burgers and 4 large orders of fries. In the first movie when ordering their food at the White Castle, Harold asked for 30 sliders, 5 french fries, and 4 large Cherry Cokes, while Kumar ordered the same except with Diet Cokes.
In Harold & Kumar Go to White Castle, Kumar's bed is just a mattress pushed up against the wall, but in this movie, set just after that one, he is packing his suitcase and has a double bed in the middle of the room.
While agent Fox is interrogating two of Harold and Kumar's friends, he undoes his belt and his pants and pulls out his shirt which is tucked in under his belt. Two seconds later, another agent comes into the room to report to Fox and Fox's belt and pants are done up straight and his shirt is tucked in nicely.
About midway through the movie, before Harold and Kumar spot the the two KKK members in the forest and right after Kumar's fantasy sex scene, when they are walking through the dark forest, you can see something metallic clearly reflecting light in the background in the woods as the camera pans sideways following the two actors. The shiny object looks like it might be a mirror of a car, since it is above the ground.
In the skydiving scene Kumar "swims" towards Harold. In free fall, you can't swim through the air, flailing your arms and legs just destabilizes yourself. To get two people together, all you have to do is face downwards and towards each other.
In the sky diving scene, Kumar holds onto Harold while Harold opens the parachute. It would be impossible for Kumar to remain holding on when the parachute opens up due to the sudden change of momentum.
Thought it is a cliché in movies, fire hydrants are not only designed to break off when hit, but need to have downward pressure applied to open the valve. So the scene in Birmingham when they backed the car over the fire hydrant and the hydrant gushed water is not realistic.
Big Bob wears an upside down rank insignia, has a style of facial hair not permitted for Army personnel, and takes his baton into the cells (which is forbidden to prevent the exact problems shown in this movie). This is to show that he is an outlaw with no respect for rules and regulations.
The guns in the movie frequently shoot many more bullets than is possible for the make's capacity. Since the movie is meant to be a live-action cartoon, where everything is larger than life, this can be seen as deliberate.
During the 'bottomless party' scene, as their buddy explains the theme of the party you see two girls walking over to a chair and a guy in a green T-shirt, also "bottomless". You can see pretty clearly that the guy is wearing a panty-hose or skin colored 'cock-sock' to cover his genitals. You can see it again about 8 seconds later.
The goof items below may give away important plot points.
When Harold and Kumar are in Alabama, the hunter that shoots and stabs the deer proceeds to claim that the deer was born in 2004. The movie takes place in 2004 (beginning at the end of Harold & Kumar Go to White Castle), and the deer is at least four years old.
When Harold and Kumar are put on the C-130 aircraft to fly back to Guantanamo Bay, there is no such airport as "Hewitt Regional Airport". The closest airport that large would be the TSTC airfield, ten minutes north of Waco, where then-President George W. Bush flew in and out of. To fly from there to Guantanamo Bay, they would fly southeast. However, when they parachute from the plane, probably half an hour out, they land in Crawford, Texas, which is an hour west of Waco.
After the credits, when Neil Patrick Harris is shown to still be alive, his car is still in the driveway of the brothel where he parked it, even though Harold and Kumar had already taken the car and are presumably long gone.
When suspects are taken into custody, they are usually patted down for any weapons that may be on that person, such as mace, to prevent them from assaulting the officers. Yet, Harold was able to hide a can of mace in his pants pocket without it being confiscated. (Possibly deliberate, as the movie repeatedly depicts authority as inept.)