(at around 1h 24 mins) When the woman jumps of the balcony to swing to another part of the theater. You can see a transparent strap holding her dress. The strap isn't visible in any other scenes.
Though the story is set in Uruguay, there is a giant flag of Argentina in the opera house.
Aircraft carriers don't have sonar systems capable of tracking submarines or launching weapons at them.
Most important livestock species in Uruguay is cattle. Goats are very rare.
The submarine was submerged but it both ran its diesel engines and transmitted a message, neither of which are possible while submerged.
In the early part of the movie when the team is going to the drop point one member pulls out personal photos, another member turns to him and says "what are you doing, you know where going in clean". The member hands off his pictures to the Chopper crew, but when they are getting out of the chopper you can see the teams names and ranks on their Kevlar Helmets, so therefore they would not be going into the mission "clean" since a clean mission would be no personal items, or identifications.
The mP5 submachine guns used throughout the movie lack a real front site. The guns look like toys.
Uruguay has had a democratic government since 1984. (In fact, since 1828, Uruguay has been a democratic republic, but there was two dictatorships, one from March 1933 to March 1938, and the last one from 1972 to 1984.)
Uruguay is a very flat country without the fjords and mountains seen in the film.
There aren't Mayan cities in South America.
While sitting at the opera viewing Tosca, the man on phone was told to look up to his left, he looks up to his right, he should have been told to look up to his right.