As the two then-surviving members of the Four Pirates of New Orleans push Parsifal's car over the cliff, there is a brief shot of what are supposed to be the driver's legs and feet working the pedals. The legs and feet are actually Parsifal's, not the driver's, as can be seen from the pants and boots.
When Big Ape lobs his scimitar at the Eurac soldiers, it is rotating clockwise from the ground. When it reaches their heads and decapitates them, it is suddenly rotating counter-clockwise from the ground.
As the ship takes off for Alpha Centauri at the end of the film, Parsifal and others are simply standing around on the ship without being strapped in. This is especially odd since the President has specifically referred to his inability to endure the g-forces during takeoff.
The scientist is said to have placed his daughter Melissa into hibernation to protect her from the effects of radiation. But merely placing her in hibernation would not protect her eggs from radiation damage, and the transparent cover of her case does not appear to consist of radiation shielding.
When the sewer rats are devouring a man alive, a close-up of a "rat" chewing on flesh reveals it to actually be a guinea pig.
Obvious stunt double for Ratchet on the wide shot when the three protagonists are riding motorcycles through the wasteland toward New York City.
Around 1 hour 14 minutes, after Big Ape says he wants to stay with the fertile girl, there is a shot of the rest of the heroes which pans to a close-up of Shorty. Behind him, a crew member is moving out of frame inside or behind part of the car.