When Serone uses dynamite to blow up a blockade across the river, a falling branch knocks the spare barrels of fuel overboard leaving them with only one for the remainder of their trip. However later the boat is seen from the back with all five barrels tied in their original position.
Sarone's rifle is a bolt action Winchester Model 70 Sporter, which requires manual cycling of the bolt to fire each successive round. In the film, the actors neglected to cycle the action, firing the gun as if it was a semi-automatic.
Near the middle of the film, when the monkeys are "warning" the documentary makers, you can see in close-up shots that several of the monkeys are tethered to the branches they are perched on with a fine cord.
After the first anaconda breaks through the glass to get Terri, Serone shoots the snake in the mouth with a tranquilizer dart. As the snake reacts to the dart, you can clearly see the wires under him that are controlling his actions.
The goof items below may give away important plot points.
Crew or equipment visible
When Serone fishes for the anaconda and the struggle starts, he sends Gary to put the lights on the anaconda. Gary takes the right spotlight, but there is someone else operating the left light, yet all people are on the rear platform at that moment (Dr. Steven Cale is in his cabin, unconscious; Mateo is already dead).
At the end of the movie as a final scare we see eggs that are being hatched. Anacondas are ovoviviparous - their eggs are retained inside their bodies, without shells, until the young are fully developed, when they emerge from the mother alive.
At one point, the snake wraps itself around Gary, causing him to spin. When the snake is about to wrap itself around his arms/shoulders, the guy throws his arm out and up, and it passes through the snake.
Towards the end of the film when Jennifer Lopez's character fires several rounds into the head of the snake, she is firing a bolt action rifle but not once does she cock the weapon, and she fails to pull the trigger for the last round.