When Malcolm is in his room, packing to go to fix the dam, Ellie's left hand switches from on Malcolm's shoulder to off in between shots.
When Malcolm is saying goodbye to Ellie in their room, he cups her face in his hands and kisses her. In the next shot, his hands are not on her face.
The apes charging on horseback with automatic rifles, firing all their weapons endlessly without reloading.
At the beginning of the movie, Caesar does not have his birthmark/scar on his upper chest.
When Koba discovers the humans are stockpiling weapons, he leads his fellow apes into Fort Point, a Civil War era fort. When he gets inside the facility, the architecture looks nothing like the brick fort built in the 1850's, but more like a standard warehouse.
When Malcolm and the Apes enter and exit the BART (subway) stations, they pass through rotary turnstiles, a type that hadn't been used in the decades before 2011.
There are no hydroelectric dams in Marin County, and no rivers that could support one.
The apes are supposed to be living in the redwoods in Northern California, yet the forest resembles the Pacific Northwest.
The building the humans are living in is similar to the Southern Pacific Company building (1 Market Street), sits at the base of California Street (albeit at an angle), and has an exterior with similar features, but it has a different entrance and is completely different on the inside.
When the hydro electricity supply is turned on, the humans say they can now contact other humans on the radios, yet they already had electricity supplied by diesel-powered generators.
The apes and humans have supposedly been unaware of each other for the last two years. But the humans' generator activity (until they ran out of power and had to seek out the dam) and the apes' camp fires have been continuing during that time, and each should have been visible to the other group.
The plot hinges on the humans having no feasible power source besides the dam. There would in fact be at least three: solar power, wind power and a wood-burning power station.
With the armed checkpoint near the Golden Gate bridge, we can assume that all approaches to the city (Bay bridge, Hayward bridge, Dumbarton bridge) are likewise guarded. So how did all of the apes - particularly the ones on horseback - get into the heart of the human colony early in the film?
The humans live among high-rise buildings that must be decaying and would soon fall. They also show no signs of raising crops, even though stored food must be decaying.
Two guards at the armory checkpoint are machined gun to death, but nobody acts concerned or raises the alarm. With the level of paranoia Dreyfus had about the apes, the humans around the armory should have been on heightened alert for any future trouble. Yet no alarm was raised about two guards having been machine-gunned to death.
(at around 1h 18 mins) When Dreyfus is giving his "We are survivors" speech to the crowd, he is holding the hand-held microphone, but the bullhorn is hanging at his waist, pointing down, instead of toward the people.