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 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).
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 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.
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.
Dodge Landon is presumably 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.
The end credits give thanks for allowing the use of clips from a movie called "The French Connection II." There is no movie by this name, the actual movie is called French Connection II (1975) (there is no "the" in the title.)
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.
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.
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.
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.
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.