During the exterior scene in which Gloria is trying to convince Joan to not go to Colombia, the weather keeps changing. First there is no precipitation, then it switches back and forth several times between snow and rain.
When Jack kills the snake right over Joan's shoulder, he pulls the dead snake out from behind her and it slides along a small ridge and falls down the small ridge where it touches Joan. In the next camera shot, the snake is back up on top of the ridge.
When Jack looks at the map and reads "Devil's Fork" for the first time, the map is entirely unfolded (the compass rose is visible in the upper right corner). In the next shot, the entire right side of the map (including the compass rose) is folded back at the crease.
During the bus crash interior scene, the placard reading "Castillo de San Felipe" is seen through the windshield falling from its mount above the horns. In the subsequent bus exterior shot, the sign is still attached.
When Joan gets on the bus she closes her window. The window is not cracked. In the next scene the bus is driving along through the jungle and all the windows are closed on the right boarding side of the bus where Joan was sitting and none of the windows are damaged or cracked. Shortly thereafter Joan wakes up on the bus and the window is cracked all the way through.
When the bus crashes into Jack's Jeep, and all of the luggage goes flying off the luggage rack, Joan's blue suitcase clearly pops open when it hits the ground, spilling her clothes all over the ground. However, when she picks her suitcase back up after Jack dispatches Zolo, her suitcase is closed again and, we presume, all her clothes are still inside.
When Jack and Joan emerge on opposite sides of the river after jumping over the waterfall, Jack tells Joan to follow the sunset (West) to Cartagena. As we know the treasure is somewhere close to the middle of the Colombian Department (State) of Cordoba (reference when Jack learns about the map), she would be heading AWAY from Cartagena which is due North of Cordoba.
When the statue containing the emerald is retrieved from the milky pool in the cave, it is wrapped inside a bundle of fresh green grass inside a bag. If the gem had been under that pool long enough for a map and treasure hunt, that grass would not be green.
In the first shootout with Zolo after the bus crash, Jack fires nine shots before reloading, then fires 11 shots (nine in the gunfight and two at the jeep). The Remington 870 he carries only holds five rounds (four in the magazine and one in the chamber).
When Ralph is talking on the phone in the local police station he notices his wanted poster. The wanted poster only states Ralph with no last name. All wanted posters have first and last name on it to describe the person.
After Juan and "Little Mule" have jumped the river, the following jeep crashes and lands upside down in extremely shallow water, which, at most, is about 20-30 feet wide (as evidenced by the shot of the jeep as it lands). Judging by the slope of both banks and the shallow water, the statement that the river is impossible to cross for 200 miles in either direction is simply not true.
When Jack grabs a vine to swing to the other side of the ravine with Joan, he hits a rock wall and not only does the wall move slightly but the rock cushions his impact - which you can see flex once he hits.