Gloria the Hippo: Where are the people?
Skipper the Penguin: We killed them and ate their livers. Gotcha there, didn't I?
At the beginning of the movie, when Marty finds the snow-bullet in Alex's mouth, he puts it in the Alex thing collection, but the collection wasn't there before and it disappears after that.
There is a scene when the lemurs are showing a book called "To Serve Lemur". This is similar to one of the classic episodes of The Twilight Zone, "To Serve Man" when the "aliens" allegedly come in peace but actually want to eat the people of earth.