When the snake eats the monkey, it is supposed to be natural footage of one animal eating another. There are many leaves around the shot and one of them was very clearly added during editing to hide a device used to launch the monkey into the snake's mouth (a frame-by-frame analysis of this scene can be found on the unrated Blue Underground DVD release).
As they escape the Cannibals cave towards the end of the film and run down the rocks by a river, you can see graffiti etched onto the face of a large rock, the graffiti looks like it reads " PETER" and a hard to read date underneath.
A dummy is obviously used when Professor Foster dies by falling into the waterfall.