Daphne's scarf is purple instead of green as she, Fred and Velma look into the cave.
When Shaggy and Scooby are running away from the Jaguaro in the makeshift canoe, they appear to be going awfully fast, especially considering that they are paddling against the river's current. It is very difficult to do this on the Amazon, which in terms of water discharge, is the largest river in the world.
When Shaggy and Scooby are arguing about who should lead their search amongst the river, Shaggy suggest flipping a coin to settle the dispute. Scooby agrees, and Shaggy reaches into his pocket, as if to pull out a coin, but when we see his hand return, there is no coin. Shaggy proceeds to flip the coin, catch it, tell Scooby to call it, and look at it to see the results, whilst to the audience, it appears that there is no coin at all.
When Barney leaves after promising Fred and the girls that he'll radio for help, his boat travels backwards.
South America does not have great apes. (Although it could be argued that Mystery Inc. discovered a previously unknown species.)
Instead of entering the cave like Fred suggests they do, he, Daphne and Velma walk past it.