On the Golden Gate bridge, the police cars and officers are waiting by the end of the road, weapons drawn. One officer at the end with a handgun has it drawn, then the next shot has it holstered, then the next shot has it drawn again.
When Will is giving his presentation to the board, he states that ALZ-112 has potential to cure central nervous system diseases, yet the presentation screen behind him flashing names of diseases flashes Muscular Dystrophy which is an intrinsic muscle disease, not a CNS disease.
On the Golden Gate Bridge, Caesar stands on the roof of a Nissan Maxima and raises his hand and roars as he stops the Apes advance. In the next shot, Caesar is seen from the rear and the car is a Volkswagen Jetta.
When they first took Caesar to the redwood forest, the California license plate registration sticker for their Jeep had an expiration of June 2010. Later when they show the grown Caesar the building complex where he was born, the registration sticker is still June 2010, despite this scene taking place five years later.
When Caesar throws food in Landon's face the tray of food in his cage is full. But after Landon soaks him with the hose and walks away, the food tray is totally empty (and it was not sprayed with the hose).
In some shots on on the Golden Gate Bridge there are four lanes of traffic going one direction and two lanes going the other way, while in other shots there are three lanes of traffic going in each direction. Additionally, the movable divider pylons that separate the northbound and southbound lanes of traffic are missing from the majority of the scenes on the bridge.
When Caesar is taken to a primate shelter in San Bruno, south of San Francisco, at one point he looks through the facility's windows and sees the Golden Gate Bridge. Later he escapes from the shelter and stands on its roof, looking at the lights of downtown San Francisco. Both of these views are impossible because the San Bruno mountains, north of San Bruno, entirely block any sight of San Francisco from there.
When the apes jump on the cable car, they move down a hill where they can see the Golden Gate Bridge behind downtown. In actuality, the bridge is a distance away. There would be nowhere in San Francisco where this shot would be viable.
The movie places Muir Woods in the Marin Headlands, just to the north of the Golden Gate Bridge. In reality, they are about 5 miles to the NW of that location and the bridge is not visible because of the hills and trees in between. Additionally, the Marin Headlands are mostly wind swept grass and scrub brush and have very few trees, let alone redwood forests.
As the apes reach San Francisco Zoo to free the zoo's captive primates, there's an establishing shot through the trees showing the downtown city skyline, with the top of the Transamerica Pyramid building clearly visible. In reality the San Francisco Zoo is in the extreme south west corner of the city, on the Pacific coast, while downtown San Francisco is in the north east of the city, next to the bay. Not only are all of San Francisco's largest hills directly in between them, blocking any view of downtown from the zoo, they are also over eight miles away from each other. The shot makes it appear that there is only flat terrain between them, and that they're only about a couple of miles apart.
As the escaped apes approach and climb the radio towers on Twin Peaks, downtown San Francisco can be seen in the distance looking to be about 10 city blocks away. Several seconds later this same angle is shown, and the buildings of downtown now look to be over 1 mile away.
When Dodge Landon drags the cattle prod across the cage, we see a shower of sparks. However, if you drag a real electric cattle prod across a metal surface, you will only see blue arcing, no different than the blue arcing between the prongs.
Leaving Gene-Sys, many of the apes smash through plate glass exterior windows as high as five stories up. Even attempting to smash through one of these windows would badly injure any primate, much less then falling down up to five stories from there onto concrete.
None of the great ape species typically use brachiation (swinging by the arms to move from tree to tree) for locomotion like the apes in the movie are frequently seen doing. Instead, they will first descend to the ground from one tree before moving to another tree to climb up it.
The experimental drugs in the movie were ALZ-112 and ALZ-113. The "ALZ" prefix was in reference to what the drug was designed to treat, Alzheimer's Disease. In the pharmaceutical industry, however, drugs in development are named with a prefix that is an abbreviation for the company developing it. Since the company's name was Gen-sys, a drug name of "GNS-112" would be plausible.
The type of respirator used during the initial test of ALZ-113 requires a snug fit to the face to prevent outside air from leaking in. The character of Franklin has a thick beard, which would have broken this seal, rendering the respirator ineffective.
After the Golden Gate fight scene, all the police cars are shut up, smashed and on fire. Will gets in one that was right in the middle of the mayhem, yet it is unscratched. - There's no guarantee that everything would sustain damage despite how unlikely it would be.
The first time Will takes Caesar to the Redwoods, Caesar extends his hand in to Will, seeking permission to run off into the forest on his own. Caroline explains the gesture to Will as one of supplication, and guides Will's hand across Caesar's in a counter response gesture. At this point in the film, Caesar is three years old. It's never explained why Will has not previously witnessed this behavior from Caesar. Additionally, the supplication gesture and Will's counter gesture are learned behaviors within ape culture. Without other apes from which to learn this behavior, it's unlikely Caesar would have come up with it on his own, nor would he have understood Will's counter gesture.
While at Gene-Sys, the apes deliberately destroy all of the security cameras one by one as they make their way through the building. There is no reason why the apes would even know what security cameras are, much less be able to easily reach and disable all of them on the ceilings in the building.
The goof items below may give away important plot points.
Dodge Landon is electrocuted in a dramatic shower of sparks when he's sprayed with the water hose while holding an electric cattle prod. This is pure nonsense. There is nowhere near enough power contained within this battery powered device to electrocute somebody.
When the intelligent apes that were exposed to ALZ-112 escaped from the sanctuary, they went to the San Francisco Zoo and freed all the apes from a large exhibit area. The freed apes joined the group on their fight for freedom. However, the zoo apes had not been exposed to ALZ-112 and would not have had the intelligence to plan and organize like the transformed apes.