During Gary's regurgitation sequence, he is shown with vomit all over his shirt. A few seconds later, the vomit is gone, only to reappear seconds later.
When Gary has quit Team America and then the rest of the team leaves, Thomas Jefferson's face opens and Theodore Roosevelt's head is already open. In the next shot it is opening.
(at around 3 mins) we see the inside of Team Base for the first time. In this scene, and all later scenes in this location, both male and female characters have black eyeliner. Outside of Team Base, the characters do not have black eyeliner.
Throughout the peace Conference the giant spinning globe behind Alec Baldwin, changes position multiple times.
When Chris fires on the Korean sub, the number on the bow is 1252. The sub that fires on Chris has number 1350 on its bow. However, the next shot shows Chris passing sub #1252 with no damage to its starboard side.
Hans Blix refers to Kim Jong-Il as Mr. Il. As per Korean naming customs where the surname appears first, Kim is the surname, whereas Jong-Il is the given name.
After his show at the beginning, Gary looks in the mirror as he remembers what happened to his brother. His reflection in the mirror shows him smiling, but the expression on his face shows he is sad and has his mouth open slightly.
When the vehicles are leaving the market in Cairo, the tracks on which the vehicles travel are visible in the sand.
Multiple references to 9/11 make it clear that this movie is set in the 2000s, but when the world's leaders convene in Jong-Il Kim's palace, a sign indicates that the country Zaire is present and its representative looks like Mobutu Sese Seko with his signature leopardskin toque. Mobutu died in 1997 and Zaire was renamed the Democratic Republic of the Congo in the same year.
When Gary enters the tavern with the blue door in Cairo we see two hands holding and moving a band member.
During the scene where the team is fighting the Koreans, after Lisa says, "We lost I.N.T.E.L.L.I.G.E.N.C.E. I repeat, we have no I.N.T.E.L.L.I.G.E.N.C.E", you can see the reflection of a face in the front window of Joe's helicopter during its head on shot.
When Spotswoode first approaches Gary backstage after his musical performance, there is a camera being pointed clearly visible on the right-hand section of the vanity mirror for a few frames.
On the "I.N.T.E.L.L.I.G.E.N.C.E." map, Egypt is shown combined with Sudan.
During the gunfight at the beginning of the movie, Joe shoots the Eiffel Tower with a bazooka, causing it to fall onto, and destroy, the Arc de Triomphe. These landmarks are roughly 2 kilometres away from each other, so there is no way this would ever occur in the manner depicted.
How did Gary get to north Korea to save the team? All all the team American vehicles were already in North Korea and the flying limousine may have been taken out in the explosion even if it hadn't it doesn't show you how he got there.
When the world leaders meet at Jong-Il Kim's peace conference the sign above Tony Blair's head reads as England. Tony Blair was Prime Minister of the United Kingdom (which consists of England, Scotland, Wales and Northern Ireland), not just England.