On the boat to San Pablo, Ernesto writes in a notebook with a pencil. When he gets up to look for his bag, the notebook and pencil are gone.
At Macchu Pichu, a piece is broken off of the sundial at the Inti Huatana (Hitching Post of the Sun). The damage occurred in 2000, when a crane fell on it. In the 1950s, it was still in perfect condition.
The movie is set in the early 1950s. When Ernesto and Alberto arrive in Valparaiso, Chile, a blue floating dry-dock (the "Valparaiso III", owned by SOCIBER) is visible on the bay. It first appeared in 1985.
At the end of the movie, when Che is at the airport, a yellow GMC pickup drives by. The pickup has a 1-piece windshield, which GMC introduced after 1952.
When Ernesto and Alberto fall off the motorcycle while dodging cows, the motorcycle slides. If you look closely, you can see a rope or cable pulling it.