Factual error: At the end of the film the apes/monkeys are seen jumping clean through the EXTERIOR windows of a downtown high-rise. I know apes/monkeys are a bit stronger than humans, but this is still is highly unlikely and would not happen so easily. The exterior windows (those from floor to ceiling, or those that replace traditional exterior walls) would be triple plated, like that of a bank partition (think of 3 car windshields glued together) One would have to repeatedly bang on it with a sledgehammer before it would even crack, let along jump clean through. However, jumping through the INTERIOR windows and doors are completely realistic since those would only be double plated.
Continuity mistake: In the scene where the chopper with Jacob fly to the bridge, they shoot and kill many apes. But only moments later when Will gets into the police car to pursue Caesar, he drives through the same section of the bridge and there are no dead ape bodies nor are there any traces of blood or anything.
Factual error: Caesar the Chimpanzee spoke human words. However Great Apes' vocal chords make them unsuitable for speech as they are higher in their throats. Since the virus only affects the brain and doesn't physically change the location of the apes' vocal chords, it's impossible for Caesar to speak, no matter how smart he is.
Revealing mistake: When Caesar and the rest of chimps cross the golden gate bridge, you can see him still wearing his red sweater (when it was already ripped off at the chimps jail). You can see that twice when the camera is recording from up above the bridge.
Factual error: The car tags are the same color even after many years Caesar is born. Three years after and then five years, the car tags are still yellow.